From owner-chemistry@ccl.net Sun Feb 7 00:09:00 2010 From: "Amir Taghavi amir_taghavi14__yahoo.com" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41198-100206144101-15502-gaNt/bIrLhW/QgQiSOzzeQ(a)server.ccl.net> X-Original-From: Amir Taghavi Content-Type: multipart/alternative; boundary="0-190973887-1265485235=:14825" Date: Sat, 6 Feb 2010 11:40:35 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Amir Taghavi [amir_taghavi14%a%yahoo.com] --0-190973887-1265485235=:14825 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable --- On Sat, 2/6/10, Amir Taghavi wrote: > From: Amir Taghavi Subject: Re: CCL: NPT TIP5P, 1atm MD To: "CCL Subscribers" Date: Saturday, February 6, 2010, 4:13 PM Hi Dear Manish, In order to work in an NPT ensemble, you have to consider this that at higher times the system will converge to your desired pressure= ,=20 As usual, working in NPT ensemble has its own difficulties, you have to monitor the pressure fluctuations, and then if you average of pressure values, you will see that your pressure average smoothly will conv= erge to your desired value at higher durations of time, while saving its fluctuations. I observed your tau-values and thermostats and barostats, you have chosen good ones, the experience has shown that the better converg= es in 0.5 ps of tau-pressure, But I recommend you strongly use the higher number of water molecules (i.e. at least 500 molecules). In fact to work in such a system, you have to monitor the total energy and pressure values to ensure that reaching to equilibrium, th= en taking average of water density for those durations, finally you find that = your density has been nearly reached up to the desired value, Of course you should not have expected to reach to the real density in experimental, as all of these water molecules are models, not th= e real ones. Hope this is helpful. Regards, Amir Taghavi Nasrabadi,Tehran Univ. --- On Sat, 2/6/10, Manish Agarwal zmanish**gmail.com wrote: > From: Manish Agarwal zmanish**gmail.com Subject: CCL: NPT TIP5P, 1atm MD To: "Taghavi, Amir " Date: Saturday, February 6, 2010, 6:27 AM Sent to CCL by: Manish Agarwal [zmanish^^gmail.com] Dear CCLers, I am having trouble reproducing the density at 1 atm, 300K for TIP5P water, or for that matter any water model in the NPT ensemble using Molecular Dynamics: have tried Berendsen Thermostat and Barostat Nose-Hoover Thermostat and Barostat am using Ewald summation for electrostatics, 256 water molecules. 2000000=A0 steps, with or without velocity scaling in the beginning 1fs time step DLPOLY ver 2.19 The problem is as follows : either the pressure does not stabilize at 1atm (too low or too high) or the temperature does not maintain at 300K When both are maintained, for example Berendsen Thermostat relaxation time 0.1ps, Barostat relaxation time 0.5ps, the density does not reach 0.99g/cc; also, the energy profile with time looks too perturbed (does NOT look like a nice fluctuation about the mean). In the NVT ensemble, however, I have been able to reproduce other static(orientational order) and dynamic properties(diffusivities) - so the model seems fine. Any thoughts, suggestions are appreciated. Regards, Manish Agarwal -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-190973887-1265485235=:14825 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable


--- On Sat, 2/6/10, Amir Taghavi <= i><amir_taghavi14 a yahoo.com> wrote:

From: Amir Taghavi <amir_taghavi14 a yahoo.com>
Subject: Re: = CCL: NPT TIP5P, 1atm MD
To: "CCL Subscribers" <chemistry a ccl.net><= br>Date: Saturday, February 6, 2010, 4:13 PM

<= style>

Hi Dear Manish,

In order to work in an NPT ensemble, you have to con= sider this that at higher times the system will converge to your desired pressure= ,

As usual, working in NPT ensemble has its own diffic= ulties, you have to monitor the pressure fluctuations, and then if you average of pressure values, you will see that your pressure average smoothly will conv= erge to your desired value at higher durations of time, while saving its fluctuations.

I observed your tau-values and thermostats and baros= tats, you have chosen good ones, the experience has shown that the better converg= es in 0.5 ps of tau-pressure,

But I recommend you strongly use the higher number o= f water molecules (i.e. at least 500 molecules).

In fact to work in such a system, you have to monito= r the total energy and pressure values to ensure that reaching to equilibrium, th= en taking average of water density for those durations, finally you find that = your density has been nearly reached up to the desired value,

Of course you should not have expected to reach to t= he real density in experimental, as all of these water molecules are models, not th= e real ones.

Hope this is helpful.

Regards,

Amir Taghavi Nasrabadi,

Te= hran Univ.



--- On Sat, 2/6/10, Manish Agarwal zmanish**gmail.com <own= er-chemistry a ccl.net> wrote:

Fro= m: Manish Agarwal zmanish**gmail.com <owner-chemistry a ccl.net>
Sub= ject: CCL: NPT TIP5P, 1atm MD
To: "Taghavi, Amir " <amir_tagh= avi14 a yahoo.com>
Date: Saturday, February 6, 2010, 6:27 AM


Sent to CCL by: Manish Agarwal [zmanish^^gmail.co= m]
Dear CCLers,

I am having trouble reproducing the density at 1 = atm, 300K for TIP5P
water, or for that matter any water model in the NPT= ensemble using
Molecular Dynamics:

have tried
Berendsen Therm= ostat and Barostat
Nose-Hoover Thermostat and Barostat

am using E= wald summation for electrostatics,
256 water molecules. 2000000  st= eps, with or without velocity scaling
in the beginning 1fs time step
DLPOLY ver 2.19

The problem is as follows : either the pres= sure does not stabilize at
1atm (too low or too high) or the temperature= does not maintain at
300K
When both are maintained, for example Bere= ndsen Thermostat relaxation
time 0.1ps, Barostat relaxation time 0.5ps, = the density does not reach
0.99g/cc; also, the energy profile with time = looks too perturbed (does
NOT look like a nice fluctuation about the mea= n).

In the NVT ensemble, however, I have been able to reproduce othe= r
static(orientational order) and dynamic properties(diffusivities) - so=
the model seems fine.

Any thoughts, suggestions are appreciated.=

Regards,
Manish Agarwal
<zmanish||gmail.com>


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=0A=0A=0A=0A --0-190973887-1265485235=:14825-- From owner-chemistry@ccl.net Sun Feb 7 02:11:00 2010 From: "Guenter Grethe ggrethe- -comcast.net" To: CCL Subject: CCL: Call for Applications, CINF-FIZ Chemie Scholarships, Message-Id: <-41199-100206222602-26763-iM9bJ+Tcx8fz3SgFPJj/4A ~ server.ccl.net> X-Original-From: "Guenter Grethe" Date: Sat, 6 Feb 2010 22:25:58 -0500 Sent to CCL by: "Guenter Grethe" [ggrethe[*]comcast.net] 2010 CINF Scholarship for Scientific Excellence Sponsored by FIZ Chemie Berlin The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by FIZ Chemie Berlin is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to three scholarships valued at $1,000 each will be presented at the 240th ACS National Meeting in Boston, MA, August 22 26, 2010. Applicants must be enrolled at a certified college or university, and they will present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the new abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe~~comcast.net, that you are applying for a scholarship. Submit your abstract to http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract for CINF Scholarship for Scientific Excellence. The deadline for submitting an abstract to PACS is March 28, 2010. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by June 15, 2010. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of FIZ Chemie-CINF Scholarship for Scientific Excellence at the poster session. Guenter Grethe From owner-chemistry@ccl.net Sun Feb 7 07:08:01 2010 From: "Manish Agarwal zmanish#,#gmail.com" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41200-100207070216-28908-8HkSkQgTYHIV/8rk8x1ntA[#]server.ccl.net> X-Original-From: Manish Agarwal Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 7 Feb 2010 17:26:44 +0530 MIME-Version: 1.0 Sent to CCL by: Manish Agarwal [zmanish|*|gmail.com] Dear CCLers Excellent suggestions, that too on the weekend ... My thanks to all. I should have mentioned that I am using cubic Periodic Boundary. Here is what I intend to do: The time step of 1 fs is, in my opinion, not too low or too high for bulk water simulations at temperatures where there are no slow dynamics. I _am_ going to increase the number of molecules, and see if it changes the outcome - 500, and 1000. I am also going to increase the number of simulation timesteps - 4-6 million should suffice for the test. I will also try Nose-Hoover thermostat-barostat combination. In the past I have run Berendsen NVT simulations with tau=3D200ps with no problems - although, reviewers have complained it to be 'too high'. The large relaxation time allows for internal dynamics to be as near NVE as possible, specially near temperatures below the model's melting point. But this is my first brush with NPT. My main concern has been that I am trying to compare MD-NPT results with those obtained from MC-NPT. I will try and post my results in the next 24-48 hours... Looking forward to more discussion, Regards, and thanks again. Manish Agarwal - - - - - - - - - - - - - - - - - - - - - - - - - - - On 6 February 2010 23:02, Venable, Richard (NIH/NHLBI) E venabler!A!nhlbi.nih.gov wrote: > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler-*-nhlbi.nih.= gov] > I have to disagree. > > If there are suspected stability problems, the last thing one should do i= s to increase the timestep. > > The weak coupling scheme typified by the Berendsen thermostat and barosta= t have been justly criticized by many, including Allen and Tildesley; Nose-= Hoover extended system approaches are regarded as considerably less flawed. > > Starting from 0 K is usually not necessary, and can be ill advised in som= e programs. =A0Anything below 200 K should be just fine. > > I don't believe one can run NPT without periodic boundaries. > > -- > Rick Venable > compuational chemist > > ________________________________________ >> From: owner-chemistry+rick_venable=3D=3Dnih.gov||ccl.net [owner-chemistr= y+rick_venable=3D=3Dnih.gov||ccl.net] On Behalf Of Mahmoud A. A. Ibrahim m.= ibrahim[a]compchem.net [owner-chemistry||ccl.net] > Sent: Saturday, February 06, 2010 11:17 AM > To: Venable, Richard (NIH/NHLBI) [E] > Subject: CCL: NPT TIP5P, 1atm MD > > Dear Manish > I am not familiar with DL Ploy. > But, if you don't mind, you can have a go with the following issues to re= produce the water density: > * Use NPT ensemble with relaxation time of 2.0ps > * Use Berendsen Thermostat with 0.5ps time constant > * Use Periodic Boundary Condition (Important) > * If it is available, start your run from 0K and increase the temperature= gradually until reaches 300K. (During heating step, use constant volume bo= undary condition). > > Have a go with these issues, Good look > Sincerely; > M. Ibrahim > > > On Fri, Feb 5, 2010 at 10:27 PM, Manish Agarwal zmanish**gmail.com > w= rote: > > Sent to CCL by: Manish Agarwal [zmanish^^gmail.com] > Dear CCLers, > > I am having trouble reproducing the density at 1 atm, 300K for TIP5P > water, or for that matter any water model in the NPT ensemble using > Molecular Dynamics: > > have tried > Berendsen Thermostat and Barostat > Nose-Hoover Thermostat and Barostat > > am using Ewald summation for electrostatics, > 256 water molecules. 2000000 =A0steps, with or without velocity scaling > in the beginning 1fs time step > DLPOLY ver 2.19 > > The problem is as follows : either the pressure does not stabilize at > 1atm (too low or too high) or the temperature does not maintain at > 300K > When both are maintained, for example Berendsen Thermostat relaxation > time 0.1ps, Barostat relaxation time 0.5ps, the density does not reach > 0.99g/cc; also, the energy profile with time looks too perturbed (does > NOT look like a nice fluctuation about the mean). > > In the NVT ensemble, however, I have been able to reproduce other > static(orientational order) and dynamic properties(diffusivities) - so > the model seems fine. > > Any thoughts, suggestions are appreciated. > > Regards, > Manish Agarwal > > > > > > -=3D This is automatically added to each message by the mailing script = =3D- > E-mail to subscribers: CHEMISTRY{=3Dcl.net or= use:E-mail to administrators: CHEMISTRY-REQUEST{=3Dcl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp:= //www.ccl.net/spammers.txt > > > - This is automatically added to each message by the mailing script -> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Sun Feb 7 08:18:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim**compchem.net" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41201-100207081149-26870-HVHmSqU/0XKcEjNkXQkdcw~!~server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6d7eefac37f67047f02093a Date: Sun, 7 Feb 2010 04:43:57 -0800 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim_+_compchem.net] --0016e6d7eefac37f67047f02093a Content-Type: text/plain; charset=ISO-8859-1 Dear Venable Thanks so much for your interest and comment on my reply. Sure, you have the right to disagree. But, here I *haven't* asked him to increase the time step (detection time). Relaxation time is what I asked for. The water system doesn't need a relaxation time of 0.1ps. On any way, I have mentioned at the beginning of my previous reply, I am not familiar with DLPOLY. So, I have mentioned the *general * precautions/protocol. About temperature raising, I said if it is *available*. But, it is * recommended*. Yes, you are *completely *right about Berendsen thermostat, all of us know that it leads to what is called hot solvent cold solute. But, for a *small *system of water (250 molecules), and for a short time simulation, I think will not be a problem to use it. Thanks again for your comments, and took forward to hearing more. Sincerely; M. Ibrahim On Sat, Feb 6, 2010 at 9:32 AM, Venable, Richard (NIH/NHLBI) E venabler!A! nhlbi.nih.gov wrote: > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler-*- > nhlbi.nih.gov] > I have to disagree. > > If there are suspected stability problems, the last thing one should do is > to increase the timestep. > > The weak coupling scheme typified by the Berendsen thermostat and barostat > have been justly criticized by many, including Allen and Tildesley; > Nose-Hoover extended system approaches are regarded as considerably less > flawed. > > Starting from 0 K is usually not necessary, and can be ill advised in some > programs. Anything below 200 K should be just fine. > > I don't believe one can run NPT without periodic boundaries. > > -- > Rick Venable > compuational chemist > > ________________________________________ > > From: owner-chemistry+rick_venable==nih.gov||ccl.net[owner-chemistry+rick_venable== > nih.gov||ccl.net] On Behalf Of Mahmoud A. A. Ibrahim m.ibrahim[a] > compchem.net [owner-chemistry||ccl.net] > Sent: Saturday, February 06, 2010 11:17 AM > To: Venable, Richard (NIH/NHLBI) [E] > Subject: CCL: NPT TIP5P, 1atm MD > > Dear Manish > I am not familiar with DL Ploy. > But, if you don't mind, you can have a go with the following issues to > reproduce the water density: > * Use NPT ensemble with relaxation time of 2.0ps > * Use Berendsen Thermostat with 0.5ps time constant > * Use Periodic Boundary Condition (Important) > * If it is available, start your run from 0K and increase the temperature > gradually until reaches 300K. (During heating step, use constant volume > boundary condition). > > Have a go with these issues, Good look > Sincerely; > M. Ibrahim > > > On Fri, Feb 5, 2010 at 10:27 PM, Manish Agarwal zmanish**gmail.com< > http://gmail.com> > =cl.net>> wrote: > > Sent to CCL by: Manish Agarwal [zmanish^^gmail.com] > Dear CCLers, > > I am having trouble reproducing the density at 1 atm, 300K for TIP5P > water, or for that matter any water model in the NPT ensemble using > Molecular Dynamics: > > have tried > Berendsen Thermostat and Barostat > Nose-Hoover Thermostat and Barostat > > am using Ewald summation for electrostatics, > 256 water molecules. 2000000 steps, with or without velocity scaling > in the beginning 1fs time step > DLPOLY ver 2.19 > > The problem is as follows : either the pressure does not stabilize at > 1atm (too low or too high) or the temperature does not maintain at > 300K > When both are maintained, for example Berendsen Thermostat relaxation > time 0.1ps, Barostat relaxation time 0.5ps, the density does not reach > 0.99g/cc; also, the energy profile with time looks too perturbed (does > NOT look like a nice fluctuation about the mean). > > In the NVT ensemble, however, I have been able to reproduce other > static(orientational order) and dynamic properties(diffusivities) - so > the model seems fine. > > Any thoughts, suggestions are appreciated. > > Regards, > Manish Agarwal > E-mail to subscribers: CHEMISTRY{=cl.net= > cl.net> or use:E-mail to administrators: CHEMISTRY-REQUEST{=cl.net CHEMISTRY-REQUEST{ =cl.net> or usehttp:// > www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > - This is automatically added to each message by the mailing script -> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim[-]compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016e6d7eefac37f67047f02093a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Venable
Thanks so much for your interest and comment on my reply.<= /div>
Sure, you have the right to disagree.
But, here I ha= ven't asked him to increase the time step (detection time). Relaxat= ion time is what I asked for. The water system doesn't need a relaxatio= n time of 0.1ps.
On any way, I have mentioned at the beginning of my previous reply, I = am not familiar with DLPOLY. So, I have mentioned the general=A0prec= autions/protocol.
About temperature raising, I said if it is a= vailable. But, it is recommended.
Yes, you are completely right about Berendsen thermostat, all o= f us know that it leads to what is called hot solvent cold solute. But, for= a small system of water (250 molecules), and for a short time simul= ation, I think will not be a problem to use it.
Thanks again for your comments, and took forward to hearing more.
Sincerely;
M. Ibrahim

On Sat, Feb 6, 2010 at 9:32 AM, Venable, Richard (NIH/NHLB= I) E venabler!A!nhlbi.ni= h.gov <owner-chemistry[-]ccl.net> wrote:

Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler-*-nhlbi.nih.gov]
I have to disagree.

If there are suspected stability problems, the last thing one should do is = to increase the timestep.

The weak coupling scheme typified by the Berendsen thermostat and barostat = have been justly criticized by many, including Allen and Tildesley; Nose-Ho= over extended system approaches are regarded as considerably less flawed.
Starting from 0 K is usually not necessary, and can be ill advised in some = programs. =A0Anything below 200 K should be just fine.

I don't believe one can run NPT without periodic boundaries.

--
Rick Venable
compuational chemist

________________________________________
> From: owner-chemistry+rick_venable=3D=3Dnih.gov||cc= l.net [owner-chemistry+rick_venable=3D=3Dnih.gov||cc= l.net] On Behalf Of Mahmoud A. A. Ibrahim m.ibrahim[a]compchem.net [owner-chemistry||ccl.net]
Sent: Saturday, February 06, 2010 11:17 AM
To: Venable, Richard (NIH/NHLBI) [E]
Subject: CCL: NPT TIP5P, 1atm MD

Dear Manish
I am not familiar with DL Ploy.
But, if you don't mind, you can have a go with the following issues to = reproduce the water density:
* Use NPT ensemble with relaxation time of 2.0ps
* Use Berendsen Thermostat with 0.5ps time constant
* Use Periodic Boundary Condition (Important)
* If it is available, start your run from 0K and increase the temperature g= radually until reaches 300K. (During heating step, use constant volume boun= dary condition).

Have a go with these issues, Good look
Sincerely;
M. Ibrahim


On Fri, Feb 5, 2010 at 10:27 PM, Manish Agarwal zmanish**gmail.com<http://gmail.com> <owner-chemistry{=3Dcl.net<mailto:owner-chemistry{=3Dcl.net>> wrote:

Sent to CCL by: Manish Agarwal [zmanish^^gmail.com<http://gmail.com>]
Dear CCLers,

I am having trouble reproducing the density at 1 atm, 300K for TIP5P
water, or for that matter any water model in the NPT ensemble using
Molecular Dynamics:

have tried
Berendsen Thermostat and Barostat
Nose-Hoover Thermostat and Barostat

am using Ewald summation for electrostatics,
256 water molecules. 2000000 =A0steps, with or without velocity scaling
in the beginning 1fs time step
DLPOLY ver 2.19

The problem is as follows : either the pressure does not stabilize at
1atm (too low or too high) or the temperature does not maintain at
300K
When both are maintained, for example Berendsen Thermostat relaxation
time 0.1ps, Barostat relaxation time 0.5ps, the density does not reach
0.99g/cc; also, the energy profile with time looks too perturbed (does
NOT look like a nice fluctuation about the mean).

In the NVT ensemble, however, I have been able to reproduce other
static(orientational order) and dynamic properties(diffusivities) - so
the model seems fine.

Any thoughts, suggestions are appreciated.

Regards,
Manish Agarwal
<zmanish||gmail.com= <http://gmail.com= >>



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY{=3Dcl.net<mailto:CHEMISTRY{=3Dcl.net= > or use:E-mail to administrators: CHEMISTRY-REQUEST{=3Dcl.net<mailto:CHEMISTRY-REQUEST{=3Dcl.net> or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spamm= ers.txt


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--
=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0= The University of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim[-]compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 Fax No.: +20862342601
--0016e6d7eefac37f67047f02093a-- From owner-chemistry@ccl.net Sun Feb 7 11:36:00 2010 From: "s. Bill s_bill36],[yahoo.co.uk" To: CCL Subject: CCL:G: G09 problem with large-core SD ECP (MWB53 for Gd) Message-Id: <-41202-100207090728-19772-z9mzxn4dAfHNW0X8wq0aRA|*|server.ccl.net> X-Original-From: "s. Bill" Content-Type: multipart/alternative; boundary="0-350405286-1265548030=:41485" Date: Sun, 7 Feb 2010 13:07:10 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: "s. Bill" [s_bill36-*-yahoo.co.uk] --0-350405286-1265548030=:41485 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Dimitri, Ibrahim and JaminI=A0haven't=A0worked before on Gadolinium, b= ut according to the electronic configuration of Gd ([Xe] 4f7 5d1 6S2), the = electronic configuration of Gd3+ is [Xe] 4f7 [NOT 4p 4s as Dimitri suggeste= d) (Reference:=A0The physics of metals and metallography=A0Vol. 102=A0Suppl= . 1=A02006).So, Ibrahim suggestion about the multiplicity of Gd3+ couldn't = be singlet is correct.May I be confused, so any declaration would be apprec= iated.S. Bill --- On Sat, 6/2/10, Jamin Krinsky jamink(a)berkeley.edu wrote: > From: Jamin Krinsky jamink(a)berkeley.edu Subject: CCL:G: G09 problem with large-core SD ECP (MWB53 for Gd) To: "Bill, S. H. " Date: Saturday, 6 February, 2010, 21:26 Dear Dimitri and Ibrahim, Dimitri is correct in that with these ECPs the trivalent ion is a singlet. = Gaussian help got back to me and it turns out that, for G09 at least, the p= roblem is with the Harris guess not being able to handle an odd number of c= ore electrons (why it works with Nd I still don't know. Below is the explan= ation and work-around proposed by Fernando: =0A If you proceed with this ECP then you will need to use =0A"guess=3Dcore", i= nstead of the default (Harris), when having an odd number=0A of core electr= ons. Note also that, at each geometry optimization step, =0Athe initial gue= ss for the wavefunction is generated using a combination =0Aof the SCF solu= tion in previous optimization step with a guess from the =0AHarris function= al. If find the same problem in a geometry optimization =0Awhen it reaches = the second step, then try to force the use of =0A"guess=3Dcore" at each geo= metry optimization step with: guess=3D(core,always) Another =0Apossibility could be to use "guess=3Dcore" for a single point ca= lculation =0Aand force the program to always read the guess from the checkp= oint file =0A("IOp(4/5=3D1)"). For instance: %chk=3Dgd.chk#p scf=3Dtight b3lyp/genecp=A0guess=3Dcore =0ATitle Card Required 3 1=0A H C O S 06-31g=0A =A0 =A0 =A0 =A0<--=A0Basis set specification for other el= ements****=0AGd 0mwb53=A0=A0 =A0 =A0 =A0<--=A0Basis set specification for G= d**** Gd 0mwb53=A0=A0 =A0=0A =A0 =A0<--=A0ECP =0Aspecification for Gd --link1--%chk=3Dgd.chk#p opt b3lyp checkbas=A0geom=3Dcheck iop(4/5=3D1) =0ATitle Card Required 3 1 Thanks much for your input. Jamin On Sat, Feb 6, 2010 at 6:29 AM, Dimitri Cavalcanti dimitricavalcanti^-^gmai= l.com wrote: =0A =0ASent to CCL by: Dimitri Cavalcanti [dimitricavalcanti#%#gmail.com] =0ADear Jamin and Ibrahim =0A =0A =A0 =A0I don't know if the behave is the same, but when i try to use th= e =0Alarge core pseudo potentials for actinides 3+ ions in gaussian03 the =0Acalculations don't go because the odd number of electrons in the ECP, =0Aso i think that happens the same for the lanthanides. In the =0Agaussian's manual is said that since the rev C.01 the use of this ECPs =0Ais possible, but i can't use it without the keyword iop(4/5=3D2) (a =0Abypass that makes gaussian ignore the odd number and runs the =0Acalculation, but takes much more time). =0A =0A =A0 About the multiplicity, there is no problem with that, using the =0A53MWB for the 3+ oxidation states the valence electrons will be the 4s =0Aand 4p orbtials, that are closed shell. =A0And about the gaussian 09 i =0Acan't help, i don't use it yet, but the link401 is the one who =0Agenerate the initial MOs, so i think that you have problems with the =0Abasis set, try put the basis set explicity, and the ECP and see what =0Ahappens, or remove the keyword "int=3Dultrafinegrid". =0A =0AGood luck and have a nice weekend. =0A =0AThe use of the 53MWB pseudopotential for gadolinium in gaussian03 =0A =0A2010/2/5 Mahmoud A. A. Ibrahim m.ibrahim]^[compchem.net =0A: =0A> Dear=A0Jamin =0A> The problem backs to the multiplicity of your ion. The Gd3+ ion CAN'T = be =0A> singlet. =0A> If you run the same job with 3 as charge and 2 as multiplicity, your j= ob =0A> will be completed without any complains. =0A> Sincerely; =0A> M. Ibrahim =0A> =0A> On Fri, Feb 5, 2010 at 10:33 AM, Jamin Krinsky jamink++berkeley.edu =0A> wrote: =0A>> =0A>> Sent to CCL by: "Jamin =A0Krinsky" [jamink _ berkeley.edu] =0A>> I'm trying to use the large core MWB53 ECP and accompanying basis for =0A>> Gd(+3) in Gaussian 09 and I'm getting the following error during init= ial =0A>> guess generation (and the job dies): =0A>> =0A>> Fell through 30 in IdenVS. =0A>> =A0Error termination via Lnk1e in /usr/software/gaussian/g09.revA02/l= 401.exe =0A>> at Sun Jan 31 16:13:55 2010 =0A>> =0A>> I have never come across this error nor can I find any online info on= it, =0A>> so I cannot figure out how to diagnose it. The analogous ECPs for Nd,= Eu, Tb =0A>> and Dy (all trivalent) work just fine, and I get the same error using= G09's =0A>> built-in ECP or pasting it in directly from the Stuttgart web site. =0A>> =0A>> Trying it on G03 (revE) results in this error: =0A>> =0A>> Odd number of core electrons in MinBas. =0A>> =A0Error termination via Lnk1e in =0A>> /usr/software/gaussian/g03_64.RevE01/g03/l401.exe at Sun Jan 31 17:11= :44 =0A>> 2010 =0A>> =0A>> Which is obvious but not very informative. =0A>> =0A>> Representative simple input: =0A>> =0A>> #p b3lyp/gen nosymm pseudo=3Dread int=3Dultrafinegrid =0A>> =0A>> large core gaussian built-in =0A>> =0A>> 3 1 =0A>> Gd =A00.0 0.0 0.0 =0A>> =0A>> Gd 0 =0A>> MWB53 =0A>> **** =0A>> =0A>> Gd 0 =0A>> MWB53 =0A>> =0A>> Any info anyone might have on this would be greatly appreciated. =0A>> =0A>> Best regards, =0A>> Jamin =0A>> =0A>> Jamin L Krinsky, Ph.D. =0A>> Molecular Graphics and Computation Facility =0A>> 175 Tan Hall, University of California, Berkeley, CA 94720 =0A>> jamink::berkeley.edu, 510-643-0616 =0A>> http://glab.cchem.berkeley.edu =0A>> =0A>> =0A>> =0A>> -=3D This is automatically added to each message by the mailing scrip= t =3D- =0A>> E-mail to subscribers: CHEMISTRY*ccl.net or use: =0A>> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A>> =0A>> E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use =0A>> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message>> =A0 =A0 = =A0http://www.ccl.net/chemistry/sub_unsub.shtml>> =A0 =A0 =A0http://www.ccl= .net/spammers.txt>> =0A=0A>> =0A> =0A> =0A> =0A> -- =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 7.05, School of Chemistry, =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0The University of Manchester, =0A> =A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL, =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom. =0A> =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Home Address =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Chemistry Department, =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty of Science, =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University, =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519, =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt. =0A> =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information =0A> =A0 =A0 =A0 =A0 =A0 Email: m.ibrahim*compchem.net =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net =0A> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +20862342601 =0A> =0A =0A =0A =0A-- =0ADimitri de Pinho Cavalcanti =0ADepartamento de Qu=EDmica Fundamental - UFPE - Br =0A+55 81 2126-8447 =0A =0A =0A =0A- This is automatically added to each message by the mailing script - =0A =0AE-mail to subscribers: CHEMISTRY%ccl.net or use: =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0AE-mail to administrators: CHEMISTRY-REQUEST%ccl.net or use =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0A=0A =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml =0A =0A=0A =0A=0A=0A =0A=0A =0A =A0 =A0 =A0http://www.ccl.net/spammers.txt =0A =0A=0A =0A =0A --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink%berkeley.edu, 510-643-0616 =0Ahttp://glab.cchem.berkeley.edu =0A=0A=0A=0A --0-350405286-1265548030=:41485 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dimitri, Ibrahim and Jamin
I ha= ven't worked before on Gadolinium, but according to the electronic con= figuration of Gd ([Xe] 4f7 5d1 6S2), the electronic configuration of Gd3+ i= s [Xe] 4f7 [NOT 4p 4s as Dimitri suggested) (Reference: The physics of= metals and metallography Vol. 102 Suppl. 1 2006).
So, Ibrahim suggestion about the multiplicity of Gd3+ couldn't be singlet = is correct.
May I be confused, so any declaration would be apprec= iated.
S. Bill

--- On Sat, 6/2/10, Jamin Krinsky jamink= (a)berkeley.edu <owner-chemistry%%ccl.net> wrote:

From: Jamin Krinsky jamink(a)berkeley.edu <owner-= chemistry%%ccl.net>
Subject: CCL:G: G09 problem with large-core SD ECP (MWB53 for Gd)
To: "Bill, S. H. " <s_bill36%%yahoo.co.uk><= br>Date: Saturday, 6 February, 2010, 21:26

Dear Dimitri and Ibrahim,

Dimitri is correct in that with these ECP= s the trivalent ion is a singlet. Gaussian help got back to me and it turns= out that, for G09 at least, the problem is with the Harris guess not being= able to handle an odd number of core electrons (why it works with Nd I sti= ll don't know. Below is the explanation and work-around proposed by Fernand= o:
=0A
If you proceed with this ECP then you will need to use =0A"gue= ss=3Dcore", instead of the default (Harris), when having an odd number=0A o= f core electrons. Note also that, at each geometry optimization step, =0Ath= e initial guess for the wavefunction is generated using a combination =0Aof= the SCF solution in previous optimization step with a guess from the =0AHa= rris functional. If find the same problem in a geometry optimization =0Awhe= n it reaches the second step, then try to force the use of =0A"guess=3Dcore= " at each geometry optimization step with:

guess=3D(core,always)

Another =0Apossibility could be to = use "guess=3Dcore" for a single point calculation =0Aand force the program = to always read the guess from the checkpoint file =0A("IOp(4/5=3D1)"). For = instance:

%chk=3Dgd.chk
#p scf=3Dtight b3lyp/genecp = ;guess=3Dcore

=0A<= /div>
Title Card Required
<= div>
3 1
<Geometry= specification>
=0A

H C O S 0
6-31g=0A       &nb= sp;<-- Basis set specification for other elements
****
=0A
Gd 0
        = ;<-- Basis set speci= fication for Gd
****

Gd 0
mwb53    =0A &nbs= p;  <-- ECP =0Aspe= cification for Gd
--link1--
%chk=3Dgd.chk
#p opt b3lyp checkbas geom=3Dcheck iop(4/5=3D1)=

=0A
Title Card Required

3= 1

Thanks much for your input.

Jamin
<= br>
On Sat, Feb 6, 2010 at 6:29 AM, Dimitri C= avalcanti dimitricavalcanti^-^gmail.com <owner-chemistry%ccl.net> = wrote:
=0A

=0ASe= nt to CCL by: Dimitri Cavalcanti [dimitricavalcanti#%#gmail.com]
=0ADear Jamin = and Ibrahim
=0A
=0A    I don't know if the behave is the sa= me, but when i try to use the
=0Alarge core pseudo potentials for actini= des 3+ ions in gaussian03 the
=0Acalculations don't go because the odd n= umber of electrons in the ECP,
=0Aso i think that happens the same for t= he lanthanides. In the
=0Agaussian's manual is said that since the rev C= .01 the use of this ECPs
=0Ais possible, but i can't use it without the = keyword iop(4/5=3D2) (a
=0Abypass that makes gaussian ignore the odd num= ber and runs the
=0Acalculation, but takes much more time).
=0A
= =0A   About the multiplicity, there is no problem with that, using the=
=0A53MWB for the 3+ oxidation states the valence electrons will be the = 4s
=0Aand 4p orbtials, that are closed shell.  And about the gaussi= an 09 i
=0Acan't help, i don't use it yet, but the link401 is the one wh= o
=0Agenerate the initial MOs, so i think that you have problems with th= e
=0Abasis set, try put the basis set explicity, and the ECP and see wha= t
=0Ahappens, or remove the keyword "int=3Dultrafinegrid".
=0A
=0A= Good luck and have a nice weekend.
=0A
=0AThe use of the 53MWB pseudo= potential for gadolinium in gaussian03
=0A
=0A2010/2/5 Mahmoud A. A. = Ibrahim m.ibrahim]^[compchem.net
=0A<owner-chemistry**ccl.net>:
=0A> Dear=  Jamin
=0A> The problem backs to the multiplicity of your ion. T= he Gd3+ ion CAN'T be
=0A> singlet.
=0A> If you run the same job= with 3 as charge and 2 as multiplicity, your job
=0A> will be comple= ted without any complains.
=0A> Sincerely;
=0A> M. Ibrahim
= =0A>
=0A> On Fri, Feb 5, 2010 at 10:33 AM, Jamin Krinsky jamink++<= a rel=3D"nofollow" target=3D"_blank" href=3D"http://berkeley.edu">berkeley.= edu
=0A> <owner-chemistry*ccl.net> wrote:
=0A>>
=0A>&= gt; Sent to CCL by: "Jamin  Krinsky" [jamink _ berkeley.edu]
=0A>>= ; I'm trying to use the large core MWB53 ECP and accompanying basis for
= =0A>> Gd(+3) in Gaussian 09 and I'm getting the following error durin= g initial
=0A>> guess generation (and the job dies):
=0A>>= ;
=0A>> Fell through 30 in IdenVS.
=0A>>  Error term= ination via Lnk1e in /usr/software/gaussian/g09.revA02/l401.exe
=0A>&= gt; at Sun Jan 31 16:13:55 2010
=0A>>
=0A>> I have never = come across this error nor can I find any online info on it,
=0A>>= so I cannot figure out how to diagnose it. The analogous ECPs for Nd, Eu, = Tb
=0A>> and Dy (all trivalent) work just fine, and I get the same= error using G09's
=0A>> built-in ECP or pasting it in directly fr= om the Stuttgart web site.
=0A>>
=0A>> Trying it on G03 (= revE) results in this error:
=0A>>
=0A>> Odd number of co= re electrons in MinBas.
=0A>>  Error termination via Lnk1e in=
=0A>> /usr/software/gaussian/g03_64.RevE01/g03/l401.exe at Sun Ja= n 31 17:11:44
=0A>> 2010
=0A>>
=0A>> Which is ob= vious but not very informative.
=0A>>
=0A>> Representativ= e simple input:
=0A>>
=0A>> #p b3lyp/gen nosymm pseudo=3D= read int=3Dultrafinegrid
=0A>>
=0A>> large core gaussian = built-in
=0A>>
=0A>> 3 1
=0A>> Gd  0.0 0.0 = 0.0
=0A>>
=0A>> Gd 0
=0A>> MWB53
=0A>> = ****
=0A>>
=0A>> Gd 0
=0A>> MWB53
=0A>>=
=0A>> Any info anyone might have on this would be greatly appreci= ated.
=0A>>
=0A>> Best regards,
=0A>> Jamin
= =0A>>
=0A>> Jamin L Krinsky, Ph.D.
=0A>> Molecular = Graphics and Computation Facility
=0A>> 175 Tan Hall, University o= f California, Berkeley, CA 94720
=0A>> jamink::berkeley.edu, 510-643-0= 616
=0A>> http://glab.cchem.berkeley.edu
=0A>>
= =0A>>
=0A>>
=0A>> -=3D This is automatically added = to each message by the mailing script =3D-
=0A>> E-mail to subscri= bers: CHEMISTRY*ccl.net or use:
=0A>>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=0A>>
= =0A>> E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use
=0A>>= ;      http://www.ccl.net/cgi-bin/ccl/se= nd_ccl_message>>      http://ww= w.ccl.net/chemistry/sub_unsub.shtml>>      ht= tp://www.ccl.net/spammers.txt>>
=0A=0A>>
=0A>
= =0A>
=0A>
=0A> --
=0A>         &nb= sp;        Mahmoud A. A. Ibrahim
=0A>   &nbs= p;                   Current A= ddress
=0A>                 7= .05, School of Chemistry,
=0A>           &nb= sp;  The University of Manchester,
=0A>       &nb= sp; Oxford Road, Manchester, M13 9PL,
=0A>        = ;               United Kingdom.
=0A&g= t;
=0A>                  = ;      Home Address
=0A>         &= nbsp;        Chemistry Department,
=0A>   &n= bsp;                 Faculty of Sci= ence,
=0A>                 &n= bsp;      Minia University,
=0A>       =                     Minia= 61519,
=0A>                 =                Egypt.
=0A>=0A>                   &nb= sp; Contact Information
=0A>           Email= : m.ibrahim*compchem.net
=0A>             &= nbsp;Website: www.compchem.net
=0A>          = ;         Fax No.: +20862342601
=0A>
=0A
= =0A
=0A
=0A--
=0ADimitri de Pinho Cavalcanti
=0ADepartamento de= Qu=EDmica Fundamental - UFPE - Br
=0A+55 81 2126-8447
=0A
=0A
= =0A
=0A- This is automatically added to each message by the mailing scri= pt -
=0A
=0AE-mail to subscribers: CHEMISTRY%ccl.net or use:
=0A      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=0A=0AE-mail to administrators: CHEMISTRY-REQUEST%ccl.net or use
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=0A      http://www.ccl.net/chemistry/sub_unsub.shtml
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=0ABefore = posting, check wait time at: http://www.ccl.net
=0A
=0AJob: http://www.ccl.net= /jobs
=0AConferences: http://server.c= cl.net/chemistry/announcements/conferences/
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=0A
=0A
=0A


--
Jamin L Krinsky, Ph.D.
Molecular Graphics and = Computation Facility
175 Tan Hall, University of California, Berkeley, C= A 94720
jamink%berkeley.= edu, 510-643-0616
=0Ahttp://glab.cchem.berkeley.edu

= =0A

=0A=0A=0A=0A --0-350405286-1265548030=:41485-- From owner-chemistry@ccl.net Sun Feb 7 13:20:01 2010 From: "Elaine Meng meng[#]cgl.ucsf.edu" To: CCL Subject: CCL: software to list chi1 angles Message-Id: <-41203-100207115913-2354-HZ2xWl9tZlzbiVvJMwM6ig(!)server.ccl.net> X-Original-From: "Elaine Meng" Date: Sun, 7 Feb 2010 11:59:09 -0500 Sent to CCL by: "Elaine Meng" [meng*o*cgl.ucsf.edu] Hi Reynier, In Chimera, you could do this by (a) opening the protein structure ("File... Open" or "File... Fetch by ID") (b) choosing "Tools... Depiction... Render by Attribute" (c) from the Render dialog, choosing "File... Save Attributes" (d) in that file save dialog, specify saving Attribute: of "residues" (instead of "atoms") named "chi1", output filename and location That gives a plain text file with contents like: attribute: chi1 recipient: residues :1.A 155.14827579618091 :2.A 173.65904867904251 :3.A 161.03647418613772 :4.A -61.545841796253114 [... etc.] Chimera is free for noncommercial use. For info and download see http://www.cgl.ucsf.edu/chimera/index.html Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Sun Feb 7 15:38:01 2010 From: "Amir Taghavi amir_taghavi14~!~yahoo.com" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41204-100207143000-11867-1Jy9AKAxtkH7ND+FZNkLqQ(!)server.ccl.net> X-Original-From: Amir Taghavi Content-Type: multipart/alternative; boundary="0-857837389-1265570973=:47024" Date: Sun, 7 Feb 2010 11:29:33 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Amir Taghavi [amir_taghavi14 a yahoo.com] --0-857837389-1265570973=:47024 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable --- On Sun, 2/7/10, Manish Agarwal zmanish#,#gmail.com wrote: > From: Manish Agarwal zmanish#,#gmail.com Subject: CCL: NPT TIP5P, 1atm MD To: "Taghavi, Amir " Date: Sunday, February 7, 2010, 11:56 AM Sent to CCL by: Manish Agarwal [zmanish|*|gmail.com] Dear CCLers Excellent suggestions, that too on the weekend ... My thanks to all. I should have mentioned=A0 that I am using cubic Periodic Boundary. Here is what I intend to do: The time step of 1 fs is, in my opinion, not too low or too high for bulk water simulations at temperatures where there are no slow dynamics. >> Even more, you can increase up to 2 fs for larger time consumption, anot= her thing is that you can use "Rattle" or "Shake" algorithms to save your c= omputation time... I _am_ going to increase the number of molecules, and see if it changes the outcome - 500, and 1000. I am also going to increase the number of simulation timesteps - 4-6 million should suffice for the test. I will also try Nose-Hoover thermostat-barostat combination. In the past I have run Berendsen NVT simulations with tau=3D200ps with no problems - although, reviewers have complained it to be 'too high'. The large relaxation time allows for internal dynamics to be as near NVE as possible, specially near temperatures below the model's melting point. But this is my first brush with NPT. >>It's abnormally too high,=20 My main concern has been that I am trying to compare MD-NPT results with those obtained from MC-NPT. >> in long times,according to ergodicity hypothesis, you will come to nearl= y same results I will try and post my results in the next 24-48 hours... Looking forward to more discussion, Regards, and thanks again. Manish Agarwal - - - - - - - - - - - - - - - - - - - - - - - - - - - On 6 February 2010 23:02, Venable, Richard (NIH/NHLBI) E venabler!A!nhlbi.nih.gov wrote: > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler-*-nhlbi.nih.= gov] > I have to disagree. > > If there are suspected stability problems, the last thing one should do i= s to increase the timestep. > > The weak coupling scheme typified by the Berendsen thermostat and barosta= t have been justly criticized by many, including Allen and Tildesley; Nose-= Hoover extended system approaches are regarded as considerably less flawed. > > Starting from 0 K is usually not necessary, and can be ill advised in som= e programs. =A0Anything below 200 K should be just fine. > > I don't believe one can run NPT without periodic boundaries. > > -- > Rick Venable > compuational chemist > > ________________________________________ >> From: owner-chemistry+rick_venable=3D=3Dnih.gov||ccl.net [owner-chemistr= y+rick_venable=3D=3Dnih.gov||ccl.net] On Behalf Of Mahmoud A. A. Ibrahim m.= ibrahim[a]compchem.net [owner-chemistry||ccl.net] > Sent: Saturday, February 06, 2010 11:17 AM > To: Venable, Richard (NIH/NHLBI) [E] > Subject: CCL: NPT TIP5P, 1atm MD > > Dear Manish > I am not familiar with DL Ploy. > But, if you don't mind, you can have a go with the following issues to re= produce the water density: > * Use NPT ensemble with relaxation time of 2.0ps > * Use Berendsen Thermostat with 0.5ps time constant > * Use Periodic Boundary Condition (Important) > * If it is available, start your run from 0K and increase the temperature= gradually until reaches 300K. (During heating step, use constant volume bo= undary condition). > > Have a go with these issues, Good look > Sincerely; > M. Ibrahim > > > On Fri, Feb 5, 2010 at 10:27 PM, Manish Agarwal zmanish**gmail.com > w= rote: > > Sent to CCL by: Manish Agarwal [zmanish^^gmail.com] > Dear CCLers, > > I am having trouble reproducing the density at 1 atm, 300K for TIP5P > water, or for that matter any water model in the NPT ensemble using > Molecular Dynamics: > > have tried > Berendsen Thermostat and Barostat > Nose-Hoover Thermostat and Barostat > > am using Ewald summation for electrostatics, > 256 water molecules. 2000000 =A0steps, with or without velocity scaling > in the beginning 1fs time step > DLPOLY ver 2.19 > > The problem is as follows : either the pressure does not stabilize at > 1atm (too low or too high) or the temperature does not maintain at > 300K > When both are maintained, for example Berendsen Thermostat relaxation > time 0.1ps, Barostat relaxation time 0.5ps, the density does not reach > 0.99g/cc; also, the energy profile with time looks too perturbed (does > NOT look like a nice fluctuation about the mean). > > In the NVT ensemble, however, I have been able to reproduce other > static(orientational order) and dynamic properties(diffusivities) - so > the model seems fine. > > Any thoughts, suggestions are appreciated. > > Regards, > Manish Agarwal > > > > > > -=3D This is automatically added to each message by the mailing script = =3D- > E-mail to subscribers: CHEMISTRY{=3Dcl.net or= use:E-mail to administrators: CHEMISTRY-REQUEST{=3Dcl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp:= //www.ccl.net/spammers.txt > > > - This is automatically added to each message by the mailing script -> = =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/= chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0=A0 =A0 =A0=A0 =A0 =A0=0A=0A=0A --0-857837389-1265570973=:47024 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable


--- On Sun, 2/7/10, Manish Agarwal= zmanish#,#gmail.com <owner-chemistry%%ccl.net> wrote:
<= blockquote style=3D"border-left: 2px solid rgb(16, 16, 255); margin-left: 5= px; padding-left: 5px;">
From: Manish Agarwal zmanish#,#gmail.com <ow= ner-chemistry%%ccl.net>
Subject: CCL: NPT TIP5P, 1atm MD
To: "Tagha= vi, Amir " <amir_taghavi14%%yahoo.com>
Date: Sunday, Februa= ry 7, 2010, 11:56 AM


Sent to CCL by: Ma= nish Agarwal [zmanish|*|gmail.com]
Dear CCLers

Excellent suggesti= ons, that too on the weekend ... My thanks to all.
I should have mention= ed  that I am using cubic Periodic Boundary.

Here is what I int= end to do:

The time step of 1 fs is, in my opinion, not too low or t= oo high for
bulk water simulations at temperatures where there are no slow
dynamics.
>> Even more= , you can increase up to 2 fs for larger time consumption, another thing is= that you can use "Rattle" or "Shake" algorithms to save your computation t= ime...
I _am_ going to increase the number of molecules, and see = if it
changes the outcome - 500, and 1000.
I am also going to increas= e the number of simulation timesteps - 4-6
million should suffice for th= e test. I will also try Nose-Hoover
thermostat-barostat combination.
=
In the past I have run Berendsen NVT simulations with tau=3D200ps with<= br>no problems - although, reviewers have complained it to be 'too high'.The large relaxation time allows for internal dynamics to be as near
N= VE as possible, specially near temperatures below the model's melting
po= int. But this is my first brush with NPT= .
>>It's abnormally too high,
My main concern has be= en that I am trying to compare MD-NPT results
with those obtained from M= C-NPT.
&= gt;> in long times,according to ergodicity hypothesis, you will come to = nearly same results
I will try and post my results in the next 24= -48 hours...

Looking forward to more discussion,
Regards, and tha= nks again.
Manish Agarwal
- - - - - - - - - - - - - - - - - - - - - -= - - - - -


On 6 February 2010 23:02, Venable, Richard (NIH/NHLBI= ) E
venabler!A!nhlbi.nih.gov <owner-chemistry . ccl.net> wrote:>
> Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler-= *-nhlbi.nih.gov]
> I have to disagree.
>
> If there are s= uspected stability problems, the last thing one should do is to increase th= e timestep.
>
> The weak coupling scheme typified by the Berendsen thermostat and barostat have been justly criticized by many, inc= luding Allen and Tildesley; Nose-Hoover extended system approaches are rega= rded as considerably less flawed.
>
> Starting from 0 K is usua= lly not necessary, and can be ill advised in some programs.  Anything = below 200 K should be just fine.
>
> I don't believe one can ru= n NPT without periodic boundaries.
>
> --
> Rick Venable<= br>> compuational chemist
>
> ______________________________= __________
>> From: owner-chemistry+rick_venable=3D=3Dnih.gov||ccl= .net [owner-chemistry+rick_venable=3D=3Dnih.gov||ccl.net] On Behalf Of Mahm= oud A. A. Ibrahim m.ibrahim[a]compchem.net [owner-chemistry||ccl.net]
&g= t; Sent: Saturday, February 06, 2010 11:17 AM
> To: Venable, Richard = (NIH/NHLBI) [E]
> Subject: CCL: NPT TIP5P, 1atm MD
>
> De= ar Manish
> I am not familiar with DL Ploy.
> But, if you don't mind, you can have a go with the following issues to reproduce the water d= ensity:
> * Use NPT ensemble with relaxation time of 2.0ps
> * = Use Berendsen Thermostat with 0.5ps time constant
> * Use Periodic Bo= undary Condition (Important)
> * If it is available, start your run f= rom 0K and increase the temperature gradually until reaches 300K. (During h= eating step, use constant volume boundary condition).
>
> Have = a go with these issues, Good look
> Sincerely;
> M. Ibrahim
= >
>
> On Fri, Feb 5, 2010 at 10:27 PM, Manish Agarwal zmanis= h**gmail.com<http://gmail= .com> <owner-chemistry{=3Dcl.net<mailto:owner-chemistry{=3Dcl.= net>> wrote:
>
> Sent to CCL by: Manish Agarwal [zmanish^= ^gmail.com<http://gmail.c= om>]
> Dear CCLers,
>
> I am having trouble reprod= ucing the density at 1 atm, 300K for TIP5P
> water, or for that matter any= water model in the NPT ensemble using
> Molecular Dynamics:
><= br>> have tried
> Berendsen Thermostat and Barostat
> Nose-H= oover Thermostat and Barostat
>
> am using Ewald summation for = electrostatics,
> 256 water molecules. 2000000  steps, with or w= ithout velocity scaling
> in the beginning 1fs time step
> DLPO= LY ver 2.19
>
> The problem is as follows : either the pressure= does not stabilize at
> 1atm (too low or too high) or the temperatur= e does not maintain at
> 300K
> When both are maintained, for e= xample Berendsen Thermostat relaxation
> time 0.1ps, Barostat relaxat= ion time 0.5ps, the density does not reach
> 0.99g/cc; also, the ener= gy profile with time looks too perturbed (does
> NOT look like a nice= fluctuation about the mean).
>
> In the NVT ensemble, however, I have been able to reproduce other
> static(orientational = order) and dynamic properties(diffusivities) - so
> the model seems f= ine.
>
> Any thoughts, suggestions are appreciated.
>
= > Regards,
> Manish Agarwal
> <zmanish||gmail.com<http://gmail.com>>
= >
>
>
> -=3D This is automatically added to each messa= ge by the mailing script =3D-
> E-mail to subscribers: CHEMISTRY{=3Dc= l.net<mailto:CHEMISTRY{=3Dcl.net> or use:E-mail to administrators: CH= EMISTRY-REQUEST{=3Dcl.net<mailto:CHEMISTRY-REQUEST{=3Dcl.net> or use<= a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/sp= ammers.txt" target=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtmlh= ttp://www.ccl.net/spammers.txt
>
>
> - This is automa= tically added to each message by the mailing script ->     &nb= sp;http://www.ccl.net/cgi-bin/ccl/send_ccl_message>     &nbs= p;http://www.ccl.net/cgi-bin/ccl/send_ccl_message>     =  http://www.ccl.net/chemistry/sub_unsub.shtml>     &n= bsp;http://ww= w.ccl.net/spammers.txt>
>
>



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=

=0A=0A --0-857837389-1265570973=:47024-- From owner-chemistry@ccl.net Sun Feb 7 16:12:01 2010 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas(0)chem.elte.hu" To: CCL Subject: CCL:G: G03 Geometry Optimization Fails Message-Id: <-41205-100207155546-26530-ZhcOyNEMt7ZcUhuppo7I5w%server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-15" Date: Sun, 7 Feb 2010 21:55:33 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas]^[chem.elte.hu] Hi Veronica, It is not easy to judge what could happen, however, Opt=3DZ-matrix does not= look=20 fine to me. Is there any reason using Z-matrix instead of the default=20 redundant internals? Redundant internals have been invented and implemented= =20 for purpose and they are the default because they are better then other=20 cooridnate systems in vast majority of cases for Geomtry optimization. I do= =20 not know about your system to give advices, but I personally use Opt=3DGDII= S=20 with G03 and it usually helps convergence. Best wishes, Odon Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry E=F6tv=F6s Lor=E1nd University, Budapest 1/A P=E1zm=E1ny P=E9ter s=E9t=E1ny H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Saturday 06 February 2010 21:10:48 veronica ferraresi=20 veroferraresi]*[gmail.com wrote: > I'd use scf(xqc) > Vero. > > On 6 February 2010 11:28, yahoo.com < > > owner-chemistry\a/ccl.net> wrote: > > Dear All, > > I tried to do a geometry optimization in Gaussian 03 on a molecule > > consist of 26 atoms of H and C. The simulation ends abnormally after so= me > > time ( about an hour). I used > > #P HF/6-31G(d) opt=3Dz-matrix Charge Nosymm in the route section. > > > > The molecule has been described in Cartesian coordinates. Here is what I > > have in the end of the output file: > > > > Error termination request processed by link 9999. > > Error termination via Lnk1e in c:\program files\Gaussian\l9999.exe at > > Sat Feb 06 17:14:40 2010. > > Job cpu time: 0 days 2 hours 39 minutes 52.0 seconds. > > File lengths (MBytes): RWF=3D 28 Int=3D 0 D2E=3D 0 Chk= =3D 9 > > Scr=3D 1 > > > > Could anyone give me some hints to solve the problem? > > Thank you in advance. From owner-chemistry@ccl.net Sun Feb 7 20:38:01 2010 From: "Jamin Krinsky jamink^^^berkeley.edu" To: CCL Subject: CCL:G: G09 problem with large-core SD ECP (MWB53 for Gd) Message-Id: <-41206-100207201624-23340-3w4cZmIhVF5B+uY+2WxrbA~!~server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00151750e6e0f1a884047f0c8bed Date: Sun, 7 Feb 2010 17:16:11 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink]_[berkeley.edu] --00151750e6e0f1a884047f0c8bed Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi S. Bill, In the context of real electron configurations Gd3+ cannot be a singlet, bu= t these ECPs put those seven unpaired "electrons" in the core, as part of the potential felt by the explicit valence electrons (only the core 5s/5p electrons in this basis when considering the free trication). So those 7 4f electrons don't contribute to the multiplicity in the calculation, the calculation only uses electrons that actually exist (and have basis functions). I guess the result could be considered similar to the way ADF calculates closed-shell atom fragments using fractional occupations: maybe it's OK to think of it as 3.5 alpha and 3.5 beta f electrons in the core bu= t I don't think this is anywhere near rigorously correct. The physical meanin= g of this is dubious, which is probably the reason for this debate. However, the simplification makes calculations on large lanthanide complexes much more doable, and lots of properties that don't depend much on the electronics of the metal are reproduced pretty well. Jamin On Sun, Feb 7, 2010 at 5:07 AM, s. Bill s_bill36],[yahoo.co.uk < owner-chemistry(a)ccl.net> wrote: > Dear Dimitri, Ibrahim and Jamin > I haven't worked before on Gadolinium, but according to the electronic > configuration of Gd ([Xe] 4f7 5d1 6S2), the electronic configuration of G= d3+ > is [Xe] 4f7 [NOT 4p 4s as Dimitri suggested) (Reference: The physics of > metals and metallography Vol. 102 Suppl. 1 2006). > So, Ibrahim suggestion about the multiplicity of Gd3+ couldn't be singlet > is correct. > May I be confused, so any declaration would be appreciated. > S. Bill > > --- On *Sat, 6/2/10, Jamin Krinsky jamink(a)berkeley.edu ccl.net>* wrote: > > > From: Jamin Krinsky jamink(a)berkeley.edu > Subject: CCL:G: G09 problem with large-core SD ECP (MWB53 for Gd) > To: "Bill, S. H. " > Date: Saturday, 6 February, 2010, 21:26 > > Dear Dimitri and Ibrahim, > > Dimitri is correct in that with these ECPs the trivalent ion is a singlet= . > Gaussian help got back to me and it turns out that, for G09 at least, the > problem is with the Harris guess not being able to handle an odd number o= f > core electrons (why it works with Nd I still don't know. Below is the > explanation and work-around proposed by Fernando: > > If you proceed with this ECP then you will need to use "guess=3Dcore", > instead of the default (Harris), when having an odd number of core > electrons. Note also that, at each geometry optimization step, the initia= l > guess for the wavefunction is generated using a combination of the SCF > solution in previous optimization step with a guess from the Harris > functional. If find the same problem in a geometry optimization when it > reaches the second step, then try to force the use of "guess=3Dcore" at e= ach > geometry optimization step with: > > guess=3D(core,always) > > Another possibility could be to use "guess=3Dcore" for a single point > calculation and force the program to always read the guess from the > checkpoint file ("IOp(4/5=3D1)"). For instance: > > %chk=3Dgd.chk > #p scf=3Dtight b3lyp/genecp guess=3Dcore > > Title Card Required > > 3 1 > > > H C O S 0 > 6-31g <-- Basis set specification for other elements > **** > Gd 0 > mwb53 <-- Basis set specification for Gd > **** > > Gd 0 > mwb53 <-- ECP specification for Gd > > --link1-- > %chk=3Dgd.chk > #p opt b3lyp checkbas geom=3Dcheck iop(4/5=3D1) > > Title Card Required > > 3 1 > > Thanks much for your input. > > Jamin > > > On Sat, Feb 6, 2010 at 6:29 AM, Dimitri Cavalcanti dimitricavalcanti^-^ > gmail.com > > wrote: > >> >> Sent to CCL by: Dimitri Cavalcanti [dimitricavalcanti#%#gmail.com] >> Dear Jamin and Ibrahim >> >> I don't know if the behave is the same, but when i try to use the >> large core pseudo potentials for actinides 3+ ions in gaussian03 the >> calculations don't go because the odd number of electrons in the ECP, >> so i think that happens the same for the lanthanides. In the >> gaussian's manual is said that since the rev C.01 the use of this ECPs >> is possible, but i can't use it without the keyword iop(4/5=3D2) (a >> bypass that makes gaussian ignore the odd number and runs the >> calculation, but takes much more time). >> >> About the multiplicity, there is no problem with that, using the >> 53MWB for the 3+ oxidation states the valence electrons will be the 4s >> and 4p orbtials, that are closed shell. And about the gaussian 09 i >> can't help, i don't use it yet, but the link401 is the one who >> generate the initial MOs, so i think that you have problems with the >> basis set, try put the basis set explicity, and the ECP and see what >> happens, or remove the keyword "int=3Dultrafinegrid". >> >> Good luck and have a nice weekend. >> >> The use of the 53MWB pseudopotential for gadolinium in gaussian03 >> >> 2010/2/5 Mahmoud A. A. Ibrahim m.ibrahim]^[compchem.net >> : >> > Dear Jamin >> > The problem backs to the multiplicity of your ion. The Gd3+ ion CAN'T = be >> > singlet. >> > If you run the same job with 3 as charge and 2 as multiplicity, your j= ob >> > will be completed without any complains. >> > Sincerely; >> > M. Ibrahim >> > >> > On Fri, Feb 5, 2010 at 10:33 AM, Jamin Krinsky jamink++berkeley.edu >> > wrote: >> >> >> >> Sent to CCL by: "Jamin Krinsky" [jamink _ berkeley.edu] >> >> I'm trying to use the large core MWB53 ECP and accompanying basis for >> >> Gd(+3) in Gaussian 09 and I'm getting the following error during >> initial >> >> guess generation (and the job dies): >> >> >> >> Fell through 30 in IdenVS. >> >> Error termination via Lnk1e in >> /usr/software/gaussian/g09.revA02/l401.exe >> >> at Sun Jan 31 16:13:55 2010 >> >> >> >> I have never come across this error nor can I find any online info on >> it, >> >> so I cannot figure out how to diagnose it. The analogous ECPs for Nd, >> Eu, Tb >> >> and Dy (all trivalent) work just fine, and I get the same error using >> G09's >> >> built-in ECP or pasting it in directly from the Stuttgart web site. >> >> >> >> Trying it on G03 (revE) results in this error: >> >> >> >> Odd number of core electrons in MinBas. >> >> Error termination via Lnk1e in >> >> /usr/software/gaussian/g03_64.RevE01/g03/l401.exe at Sun Jan 31 >> 17:11:44 >> >> 2010 >> >> >> >> Which is obvious but not very informative. >> >> >> >> Representative simple input: >> >> >> >> #p b3lyp/gen nosymm pseudo=3Dread int=3Dultrafinegrid >> >> >> >> large core gaussian built-in >> >> >> >> 3 1 >> >> Gd 0.0 0.0 0.0 >> >> >> >> Gd 0 >> >> MWB53 >> >> **** >> >> >> >> Gd 0 >> >> MWB53 >> >> >> >> Any info anyone might have on this would be greatly appreciated. >> >> >> >> Best regards, >> >> Jamin >> >> >> >> Jamin L Krinsky, Ph.D. >> >> Molecular Graphics and Computation Facility >> >> 175 Tan Hall, University of California, Berkeley, CA 94720 >> >> jamink::berkeley.edu, 510-643-0616 >> >> http://glab.cchem.berkeley.edu >> >> >> >> >> >> >> >> -=3D This is automatically added to each message by the mailing scrip= t =3D- >> >> E-mail to subscribers: CHEMISTRY*ccl.net or use:>> >> >> >> E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use>> >> >> >> > >> > >> > >> > -- >> > Mahmoud A. A. Ibrahim >> > Current Address >> > 7.05, School of Chemistry, >> > The University of Manchester, >> > Oxford Road, Manchester, M13 9PL, >> > United Kingdom. >> > >> > Home Address >> > Chemistry Department, >> > Faculty of Science, >> > Minia University, >> > Minia 61519, >> > Egypt. >> > >> > Contact Information >> > Email: m.ibrahim*compchem.net >> > Website: www.compchem.net >> > Fax No.: +20862342601 >> > >> >> >> >> -- >> Dimitri de Pinho Cavalcanti >> Departamento de Qu=EDmica Fundamental - UFPE - Br >> +55 81 2126-8447 >> >> >> >> - This is automatically added to each message by the mailing script - >> >> E-mail to subscribers: CHEMISTRY%ccl.netor use:>> >> E-mail to administrators: CHEMISTRY-REQUEST%ccl.netor use>> >> >> > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink%berkeley.edu , > 510-643-0616 > http://glab.cchem.berkeley.edu > > > --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink(a)berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --00151750e6e0f1a884047f0c8bed Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi S. Bill,
In the context of real electron configurations Gd3+ cannot b= e a singlet, but these ECPs put those seven unpaired "electrons" = in the core, as part of the potential felt by the explicit valence electron= s (only the core 5s/5p electrons in this basis when considering the free tr= ication). So those 7 4f electrons don't contribute to the multiplicity = in the calculation, the calculation only uses electrons that actually exist= (and have basis functions). I guess the result could be considered similar= to the way ADF calculates closed-shell atom fragments using fractional occ= upations: maybe it's OK to think of it as 3.5 alpha and 3.5 beta f elec= trons in=20 the core but I don't think this is anywhere near rigorously correct. Th= e physical meaning of this is dubious, which is probably the reason for thi= s debate. However, the simplification makes calculations on large lanthanid= e complexes much more doable, and lots of properties that don't depend = much on the electronics of the metal are reproduced pretty well.
Jamin

On Sun, Feb 7, 2010 at 5:07 AM, s. = Bill s_bill36],[yahoo.co.uk <owner-chemistry(a)ccl.ne= t> wrote:
Dear Dimitri, Ibrahim and Jamin
I=A0haven't=A0worked before on Gado= linium, but according to the electronic configuration of Gd ([Xe] 4f7 5d1 6= S2), the electronic configuration of Gd3+ is [Xe] 4f7 [NOT 4p 4s as Dimitri= suggested) (Reference:=A0The physics of metals and metallography=A0Vol. 10= 2=A0Suppl. 1=A02006).
So, Ibrahim suggestion about the multiplicity of Gd3+ couldn't be = singlet is correct.
May I be confused, so any declaration would b= e appreciated.
S. Bill

--- On Sat, 6/2/10, Jamin Krinsk= y jamink(a)berkeley.edu <owner-chemistry,ccl.= net> wrote:

From: Jamin Krinsky jamink(a)berkeley.edu <owner-chemistry,ccl.net>
Subject: CCL:G: G09 problem with large-core SD ECP (MWB53 for Gd)
To: "Bill, S. H. " <s_bill36,yahoo.co.uk>
Date: Saturday, 6= February, 2010, 21:26

Dear Dimitri and Ibrahim,

Dimitri= is correct in that with these ECPs the trivalent ion is a singlet. Gaussia= n help got back to me and it turns out that, for G09 at least, the problem = is with the Harris guess not being able to handle an odd number of core ele= ctrons (why it works with Nd I still don't know. Below is the explanati= on and work-around proposed by Fernando:

If you proceed with this ECP then you will need to use=20 "guess=3Dcore", instead of the default (Harris), when having an o= dd number of core electrons. Note also that, at each geometry optimization step,=20 the initial guess for the wavefunction is generated using a combination=20 of the SCF solution in previous optimization step with a guess from the=20 Harris functional. If find the same problem in a geometry optimization=20 when it reaches the second step, then try to force the use of=20 "guess=3Dcore" at each geometry optimization step with:

guess=3D(core,always)

Anot= her=20 possibility could be to use "guess=3Dcore" for a single point cal= culation=20 and force the program to always read the guess from the checkpoint file=20 ("IOp(4/5=3D1)"). For instance:

%chk=3Dgd.chk
#p scf=3Dtight b3lyp/genecp=A0guess=3Dcore

Title Card Required

3 1
<Geometry = specification>

H C O S 0
6= -31g =A0 =A0 =A0 =A0<--=A0Basis set specification for other elemen= ts
****=
Gd 0
mwb53<= span style=3D"font-weight: normal;">=A0=A0 =A0 =A0 =A0<--=A0Basis set specification for Gd
****

Gd 0
mwb53=A0=A0 =A0 =A0 =A0<--=A0ECP=20 specification for Gd

--link1--
%= chk=3Dgd.chk
#p opt b= 3lyp checkbas=A0geom=3Dcheck iop(4/5=3D1)

Title Card Required

3 1

Thanks much for your input.

Jamin

On Sat, Feb 6, 2010 at 6:29 AM, Dimitri Cavalc= anti dimitricavalcanti^-^gmail.com <owner= -chemistry%ccl.net> wrote:

Sent to CCL by: Dimitri Cavalcanti [dimitricavalcanti#%#gmail.com]
Dear Jamin and Ibrahim

=A0 =A0I don't know if the behave is the same, but when i try to use t= he
large core pseudo potentials for actinides 3+ ions in gaussian03 the
calculations don't go because the odd number of electrons in the ECP, so i think that happens the same for the lanthanides. In the
gaussian's manual is said that since the rev C.01 the use of this ECPs<= br> is possible, but i can't use it without the keyword iop(4/5=3D2) (a
bypass that makes gaussian ignore the odd number and runs the
calculation, but takes much more time).

=A0 About the multiplicity, there is no problem with that, using the
53MWB for the 3+ oxidation states the valence electrons will be the 4s
and 4p orbtials, that are closed shell. =A0And about the gaussian 09 i
can't help, i don't use it yet, but the link401 is the one who
generate the initial MOs, so i think that you have problems with the
basis set, try put the basis set explicity, and the ECP and see what
happens, or remove the keyword "int=3Dultrafinegrid".

Good luck and have a nice weekend.

The use of the 53MWB pseudopotential for gadolinium in gaussian03

2010/2/5 Mahmoud A. A. Ibrahim m.ibrahim]^[compchem.net
<owner-chemistry**ccl.net>:
> Dear=A0Jamin
> The problem backs to the multiplicity of your ion. The Gd3+ ion CAN= 9;T be
> singlet.
> If you run the same job with 3 as charge and 2 as multiplicity, your j= ob
> will be completed without any complains.
> Sincerely;
> M. Ibrahim
>
> On Fri, Feb 5, 2010 at 10:33 AM, Jamin Krinsky jamink++berkeley.edu
> <owner-chemistry*ccl.net> wrote:
>>
>> Sent to CCL by: "Jamin =A0Krinsky" [jamink _ berkeley.edu] >> I'm trying to use the large core MWB53 ECP and accompanying ba= sis for
>> Gd(+3) in Gaussian 09 and I'm getting the following error duri= ng initial
>> guess generation (and the job dies):
>>
>> Fell through 30 in IdenVS.
>> =A0Error termination via Lnk1e in /usr/software/gaussian/g09.revA0= 2/l401.exe
>> at Sun Jan 31 16:13:55 2010
>>
>> I have never come across this error nor can I find any online info= on it,
>> so I cannot figure out how to diagnose it. The analogous ECPs for = Nd, Eu, Tb
>> and Dy (all trivalent) work just fine, and I get the same error us= ing G09's
>> built-in ECP or pasting it in directly from the Stuttgart web site= .
>>
>> Trying it on G03 (revE) results in this error:
>>
>> Odd number of core electrons in MinBas.
>> =A0Error termination via Lnk1e in
>> /usr/software/gaussian/g03_64.RevE01/g03/l401.exe at Sun Jan 31 17= :11:44
>> 2010
>>
>> Which is obvious but not very informative.
>>
>> Representative simple input:
>>
>> #p b3lyp/gen nosymm pseudo=3Dread int=3Dultrafinegrid
>>
>> large core gaussian built-in
>>
>> 3 1
>> Gd =A00.0 0.0 0.0
>>
>> Gd 0
>> MWB53
>> ****
>>
>> Gd 0
>> MWB53
>>
>> Any info anyone might have on this would be greatly appreciated. >>
>> Best regards,
>> Jamin
>>
>> Jamin L Krinsky, Ph.D.
>> Molecular Graphics and Computation Facility
>> 175 Tan Hall, University of California, Berkeley, CA 94720
>> jamink::berkeley.edu, 510-643-0616
>> http://glab.cchem.berkeley.edu
>>
>>
>>
>> -=3D This is automatically added to each message by the mailing sc= ript =3D-
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>>
>
>
>
> --
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 7.05, School of Chemistry,
> =A0 =A0 =A0 =A0 =A0 =A0 =A0The University of Manchester,
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> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.
>
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Home Address
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> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
> =A0 =A0 =A0 =A0 =A0 Email: m.ibrahim*compchem.net
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> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +20862342601
>



--
Dimitri de Pinho Cavalcanti
Departamento de Qu=EDmica Fundamental - UFPE - Br
+55 81 2126-8447



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--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink%berkeley.edu= , 510-643-0616
http://glab.cchem.berkeley.edu





--
Jamin L Krinsky, = Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, Unive= rsity of California, Berkeley, CA 94720
jamink(a)berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--00151750e6e0f1a884047f0c8bed-- From owner-chemistry@ccl.net Sun Feb 7 21:13:01 2010 From: "srikanth peddireddy srikanth.pedireddy__gmail.com" To: CCL Subject: CCL:G: G03 Geometry Optimization Fails Message-Id: <-41207-100207015302-12221-Bd2DHL1fOH6k+PZqbdHWNw()server.ccl.net> X-Original-From: srikanth peddireddy Content-Type: multipart/alternative; boundary=000e0cd1391aa77cb1047efc4bbf Date: Sun, 7 Feb 2010 11:22:52 +0530 MIME-Version: 1.0 Sent to CCL by: srikanth peddireddy [srikanth.pedireddy::gmail.com] --000e0cd1391aa77cb1047efc4bbf Content-Type: text/plain; charset=ISO-8859-1 Dear Arash, Hi, you can try by slightly changing the initial geometry of the molecule so that it may converge in given number of steps. regards Sri On Sun, Feb 7, 2010 at 3:01 AM, Jamin Krinsky jamink]-[berkeley.edu < owner-chemistry~!~ccl.net> wrote: > Dear Arash, > Almost always when I see "Error termination request processed by link 9999" > it means the optimization ran out of cycles. For a 26 atom molecule 2 hrs > sounds about right for the time this would take to happen. Look up in the > output to the last cycle and it should be obvious if this happened. Why the > explanation is separate from the actual error message I don't know. > Regards, > Jamin > > > On Sat, Feb 6, 2010 at 6:28 AM, yahoo.com < > owner-chemistry]*[ccl.net> wrote: > >> Dear All, >> I tried to do a geometry optimization in Gaussian 03 on a molecule consist >> of 26 atoms of H and C. The simulation ends abnormally after some time ( >> about an hour). I used >> #P HF/6-31G(d) opt=z-matrix Charge Nosymm in the route section. >> >> The molecule has been described in Cartesian coordinates. Here is what I >> have in the end of the output file: >> >> Error termination request processed by link 9999. >> Error termination via Lnk1e in c:\program files\Gaussian\l9999.exe at Sat >> Feb 06 17:14:40 2010. >> Job cpu time: 0 days 2 hours 39 minutes 52.0 seconds. >> File lengths (MBytes): RWF= 28 Int= 0 D2E= 0 Chk= 9 >> Scr= 1 >> >> Could anyone give me some hints to solve the problem? >> Thank you in advance. >> >> >> > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink]*[berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > --000e0cd1391aa77cb1047efc4bbf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Arash,

=A0Hi, you can try by slightly changing the initial geo= metry of the molecule so that it may converge in given number of steps.
=
regards
Sri

On Sun, Feb 7, 2010 at= 3:01 AM, Jamin Krinsky jamink]-[berkeley.e= du <own= er-chemistry~!~ccl.net> wrote:
Dear Arash,
Al= most always when I see "Error termination request processed by link 99= 99" it means the optimization ran out of cycles. For a 26 atom molecul= e 2 hrs sounds about right for the time this would take to happen. Look up = in the output to the last cycle and it should be obvious if this happened. = Why the explanation is separate from the actual error message I don't k= now.
Regards,
Jamin


On Sa= t, Feb 6, 2010 at 6:28 AM, **yahoo.com <owner-chemistry]*[ccl.n= et> wrote:
Dear All,
I tried to do a geometry optimization in Gaussian 03 on a mole= cule consist of 26 atoms of H and C. The simulation ends abnormally after s= ome time ( about an hour).=A0 I used
=A0#P HF/6-31G(d) opt=3Dz-matrix=A0= Charge Nosymm in the route section.

The molecule has been described in Cartesian coordinates. Here is what = I have in the end of the output file:

Error termination request proc= essed by link 9999.
=A0Error termination via Lnk1e in c:\program files\G= aussian\l9999.exe at Sat Feb 06 17:14:40 2010.
=A0Job cpu time:=A0 0 days=A0 2 hours 39 minutes 52.0 seconds.
=A0File l= engths (MBytes):=A0 RWF=3D=A0=A0=A0=A0 28 Int=3D=A0=A0=A0=A0=A0 0 D2E=3D=A0= =A0=A0=A0=A0 0 Chk=3D=A0=A0=A0=A0=A0 9 Scr=3D=A0=A0=A0=A0=A0 1

Could= anyone give me some hints to solve the problem?
Thank you in advance.





--
<= /div>
Jamin L Krinsky, Ph.D.
Molecular Graphics and Com= putation Facility
175 Tan Hall, University of California, Berkeley, CA 9= 4720
jamink]*[berkele= y.edu, 510-643-0616
http://glab.cc= hem.berkeley.edu


--000e0cd1391aa77cb1047efc4bbf--