From owner-chemistry@ccl.net Sat Feb 6 08:16:01 2010 From: "Manish Agarwal zmanish**gmail.com" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41183-100206022217-23076-4foyQiu2Kb4opOKG2sgn9g^_^server.ccl.net> X-Original-From: Manish Agarwal Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 6 Feb 2010 11:57:04 +0530 MIME-Version: 1.0 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 From owner-chemistry@ccl.net Sat Feb 6 08:51:00 2010 From: "aa aa*|*chemaxon.hu" To: CCL Subject: CCL: Second call for papers: ChemAxon's 2010 European UGM, May 19-20, Budapest, Hungary Message-Id: <-41184-100205153741-28864-yDenn4g0OXABGJ1p1RyB5w+/-server.ccl.net> X-Original-From: aa Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 05 Feb 2010 20:49:01 +0100 MIME-Version: 1.0 Sent to CCL by: aa [aa-x-chemaxon.hu] Excuse cross postings Good day, ChemAxon's 2010 European User Group Meeting will be held on Wednesday and Thursday, May 19-20th at the Danubius Gellert Hotel, Budapest, Hungary. The meeting will preceded by a training day on May 18th. The User Group Meeting will feature oral and poster presentations from ChemAxon users, scientists, developers and partners as well as our usual range of social events to mix, speak and enjoy with staff and peers. We are inviting those interested in presenting at the meeting to submit abstracts for review. The deadline for receipt of oral abstracts is February 26th. To find out more and submit your abstract please visit: http://www.chemaxon.com/UGM/10/index.html. The presentations archive, including original presentations and meeting reports from Wendy Warr and Yvonne Martin, is here: http://www.chemaxon.com/UGM/ugm_land.html, video from the last meeting (San Diego) is available at our vimeo UGM channel here: http://vimeo.com/channels/ugm We hope you can join us for what has proven to be a most interesting and enjoyable cheminformatics event. See you there. Alex -- *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce From owner-chemistry@ccl.net Sat Feb 6 11:13:00 2010 From: "" To: CCL Subject: CCL:G: G03 Geometry Optimization Fails Message-Id: <-41185-100206092840-12379-fuGZK7JBaxW/9fDBUWQrMg(a)server.ccl.net> X-Original-From: yahoo.com> Content-Type: multipart/alternative; boundary="0-144917176-1265466506=:76294" Date: Sat, 6 Feb 2010 06:28:26 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: yahoo.com] --0-144917176-1265466506=:76294 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable 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 ( ab= out 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 ha= ve in the end of the output file: Error termination request processed by link 9999. =A0Error termination via Lnk1e in c:\program files\Gaussian\l9999.exe at Sa= t Feb 06 17:14:40 2010. =A0Job cpu time:=A0 0 days=A0 2 hours 39 minutes 52.0 seconds. =A0File lengths (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. =0A=0A=0A --0-144917176-1265466506=:76294 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A --0-144917176-1265466506=:76294-- From owner-chemistry@ccl.net Sat Feb 6 11:48:01 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim[a]compchem.net" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41186-100206111717-3598-zAtfsLsAXu3fKNehdoFjMw : server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6d5667a1acea2047ef0e6d3 Date: Sat, 6 Feb 2010 08:17:04 -0800 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim-*-compchem.net] --0016e6d5667a1acea2047ef0e6d3 Content-Type: text/plain; charset=ISO-8859-1 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 < owner-chemistry{=}ccl.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 > > > -- 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 --0016e6d5667a1acea2047ef0e6d3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear=A0Manish=A0
I am not familiar with DL Ploy.
But, if you = don't mind, you can have a go with the following issues to reproduce th= e water density:
* Use NPT ensemble with=A0relaxation time of 2.0= ps
* Use Berendsen Thermostat with 0.5ps time constant
* Use Pe= riodic 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=A0issues, Good look
Sinc= erely;
M. Ibrahim


On= Fri, Feb 5, 2010 at 10:27 PM, Manish Agarwal zmanish**gmail.com <owner-chemistry{=}ccl.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 =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&g= t;



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY{=}ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST{=}ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
=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 =A0The Universi= ty 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 Univers= ity,
=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{=}compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601
--0016e6d5667a1acea2047ef0e6d3-- From owner-chemistry@ccl.net Sat Feb 6 12:23:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim*compchem.net" To: CCL Subject: CCL:G: G03 Geometry Optimization Fails Message-Id: <-41187-100206121130-7315-xGmpTdEeG+B0NvTg9kF44g_._server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6d7dfa708fd45047ef1a8f0 Date: Sat, 6 Feb 2010 09:11:18 -0800 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim^^^compchem.net] --0016e6d7dfa708fd45047ef1a8f0 Content-Type: text/plain; charset=ISO-8859-1 Dear Arash You don't support us with a full information about your error. I guess your error is returned to that fact that you have reached the maximum cycles number (it will be a small number by default because your molecule is small and composed of H and C only). Please, resubmit your job again with adding MaxCycle=512 If your job failed again, you would have to send us more information. Sincerely; M. Ibrahim 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. > > > -- 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 --0016e6d7dfa708fd45047ef1a8f0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear=A0Arash=A0
You don't support us with a full information about = your error.
I guess your error is returned to that fact that you = have reached the maximum cycles number (it will be a small number by defaul= t because your molecule is small and composed of H and C only).
Please, resubmit your job again with adding MaxCycle=3D512=A0
If your job failed again, you would have to send us more=A0information.
Sincerely;
M. Ibrahim

On Sat, Feb 6, 2010 at 6:28 AM, a href=3D"htt= p://yahoo.com">yahoo.com <owner-chemistry++ccl.net> wrote:
Dear All,
I tried to do a geometry optimiz= ation in Gaussian 03 on a molecule consist of 26 atoms of H and C. The simu= lation ends abnormally after some time ( about an hour).  I used
&n= bsp;#P HF/6-31G(d) opt=3Dz-matrix  Charge Nosymm in the route section.=

The molecule has been described in Cartesian coordinates. Here is w= hat 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  &nb= sp;   9 Scr=3D      1

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

Dear All,
I tried to do a geometry opt= imization in Gaussian 03 on a molecule consist of 26 atoms of H and C. The = simulation ends abnormally after some 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\Gaussian\l9999.exe at Sa= t Feb 06 17:14:40 2010.
=A0Job cpu time:=A0 0 days=A0 2 hours 39 minutes= 52.0 seconds.
=A0File lengths (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.





--
=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 =A0The Univ= ersity 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 Univers= ity,
=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++compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601
--0016e6d7dfa708fd45047ef1a8f0-- From owner-chemistry@ccl.net Sat Feb 6 12:58:00 2010 From: "jaleel uc jaleel.uc##gmail.com" To: CCL Subject: CCL:G: G03 Geometry Optimization Fails Message-Id: <-41188-100206114406-16546-dK3k6wTOvEc5LPW4t+vWmg**server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=0016e64c3eda10ff1a047ef13220 Date: Sat, 6 Feb 2010 22:08:19 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc]=[gmail.com] --0016e64c3eda10ff1a047ef13220 Content-Type: text/plain; charset=ISO-8859-1 Check the RHF/UHF selection On 2/6/10, yahoo.com 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. > > > -- Dr U.C.A.Jaleel. lecturer in cheminformatics Malabar christian college calicut --0016e64c3eda10ff1a047ef13220 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Check the RHF/UHF selection

On 2/6/10, **yahoo.com = <owner-chemistry!^!ccl.net&= gt; wrote:
Dear All,
I tried to do a geometry optimization in Ga= ussian 03 on a molecule consist of 26 atoms of H and C. The simulation ends= abnormally after some 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.



=
--
Dr U.C.A.Jaleel.
lecturer in cheminformatics
Malabar chri= stian college
calicut=20 --0016e64c3eda10ff1a047ef13220-- From owner-chemistry@ccl.net Sat Feb 6 13:33:00 2010 From: "Dimitri Cavalcanti dimitricavalcanti^-^gmail.com" To: CCL Subject: CCL:G: G09 problem with large-core SD ECP (MWB53 for Gd) Message-Id: <-41189-100206102712-31454-HVHmSqU/0XKcEjNkXQkdcw*server.ccl.net> X-Original-From: Dimitri Cavalcanti Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 6 Feb 2010 12:29:46 -0200 MIME-Version: 1.0 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=A0Jamin > 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 job > 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 =A0Krinsky" [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. >> =A0Error 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 G0= 9'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 script = =3D- >> E-mail to subscribers: CHEMISTRY*ccl.net or use: >> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message >> >> E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use >> =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>> >> > > > > -- > =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, > =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 =A0Chemistry Department, > =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty of 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 > --=20 Dimitri de Pinho Cavalcanti Departamento de Qu=EDmica Fundamental - UFPE - Br +55 81 2126-8447 From owner-chemistry@ccl.net Sat Feb 6 14:09:01 2010 From: "Amir Taghavi amir_taghavi14[*]yahoo.com" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41190-100206121324-8193-1lXP93zWATjWcqWbiIZ5WA[-]server.ccl.net> X-Original-From: Amir Taghavi Content-Type: multipart/alternative; boundary="0-779689553-1265472791=:35566" Date: Sat, 6 Feb 2010 08:13:11 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Amir Taghavi [amir_taghavi14{=}yahoo.com] --0-779689553-1265472791=:35566 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A=0A=0A=0AHi Dear Manish,=0A=0AIn order to work in an NPT ensemble, you h= ave to consider=0Athis that at higher times the system will converge to you= r desired pressure, =0A=0AAs usual, working in NPT ensemble has its own dif= ficulties,=0Ayou have to monitor the pressure fluctuations, and then if you= average of=0Apressure values, you will see that your pressure average smoo= thly will converge=0Ato your desired value at higher durations of time, whi= le saving its=0Afluctuations.=0A=0AI observed your tau-values and thermosta= ts and barostats,=0Ayou have chosen good ones, the experience has shown tha= t the better converges=0Ain 0.5 ps of tau-pressure,=0A=0ABut I recommend yo= u strongly use the higher number of water=0Amolecules (i.e. at least 500 mo= lecules).=0A=0AIn fact to work in such a system, you have to monitor the=0A= total energy and pressure values to ensure that reaching to equilibrium, th= en=0Ataking average of water density for those durations, finally you find = that your=0Adensity has been nearly reached up to the desired value,=0A=0AO= f course you should not have expected to reach to the real=0Adensity in exp= erimental, as all of these water molecules are models, not the=0Areal ones.= =0A=0AHope this is helpful.=0A=0ARegards,=0A=0AAmir Taghavi Nasrabadi,Tehra= n Univ. =0A=0A --- 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 --0-779689553-1265472791=:35566 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A

H= i Dear Manish,

=0A=0A

In order to work in an NPT e= nsemble, you have to consider=0Athis that at higher times the system will c= onverge to your desired pressure,

=0A=0A

As usual= , working in NPT ensemble has its own difficulties,=0Ayou have to monitor t= he pressure fluctuations, and then if you average of=0Apressure values, you= will see that your pressure average smoothly will converge=0Ato your desir= ed value at higher durations of time, while saving its=0Afluctuations.

= =0A=0A

I observed your tau-values and thermostats and= barostats,=0Ayou have chosen good ones, the experience has shown that the = better converges=0Ain 0.5 ps of tau-pressure,

=0A=0A

But I recommend you strongly use the higher number of water=0Amolecules = (i.e. at least 500 molecules).

=0A=0A

In fact to w= ork in such a system, you have to monitor the=0Atotal energy and pressure v= alues to ensure that reaching to equilibrium, then=0Ataking average of wate= r density for those durations, finally you find that your=0Adensity has bee= n nearly reached up to the desired value,

=0A=0A

O= f course you should not have expected to reach to the real=0Adensity in exp= erimental, as all of these water molecules are models, not the=0Areal ones.=

=0A=0A

Hope this is helpful.

=0A=0A

Regards,

=0A=0A

Amir Taghavi Nasrabadi= ,

Tehran Univ.

=0A=0A

--- On Sat= , 2/6/10, Manish Agarwal zmanish**gmail.com <owner-chemistry * ccl.net&= gt; wrote:

From: Manish Agarwal zma= nish**gmail.com <owner-chemistry * ccl.net>
Subject: CCL: NPT TIP5P,= 1atm MD
To: "Taghavi, Amir " <amir_taghavi14 * yahoo.com>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 TIP5Pwater, or for that matter any water model in the NPT ensemble using
Mo= lecular Dynamics:

have tried
Berendsen Thermostat and BarostatNose-Hoover Thermostat and Barostat

am using Ewald summation for el= ectrostatics,
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 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>


-=3D This is automatically added to each message by the mailing script= =3D-
To recover the email address of the author of the message, please = change
E-mai= l to subscribers: CHEMISTRY * ccl.net or use:
    &= nbsp; http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail = to administrators: CHEMISTRY-REQUEST * ccl.net o= r use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_me= ssage
      http://www= .ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait ti= me at: http://www.ccl.net<= /a>

Job: http://www.ccl.net/jobs=
Conferences: http://server.ccl.net/chemistry/announc= ements/conferences/

Search Messages: http://www.ccl.net/ch= emistry/searchccl/index.shtml

If your mail bounces from CCL with= 5.7.1 error, check:
      http://www.ccl.net/spammers.txt

= RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/


=0A=0A --0-779689553-1265472791=:35566-- From owner-chemistry@ccl.net Sat Feb 6 14:43:02 2010 From: "Venable, Richard (NIH/NHLBI) E venabler!A!nhlbi.nih.gov" To: CCL Subject: CCL: NPT TIP5P, 1atm MD Message-Id: <-41191-100206130442-17038-APXAUPT2ISiNCRvfz8GO2A^server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Sat, 6 Feb 2010 12:32:45 -0500 MIME-Version: 1.0 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. 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=3D=3Dnih.gov^ccl.net [owner-chemistry+ri= ck_venable=3D=3Dnih.gov^ccl.net] On Behalf Of Mahmoud A. A. Ibrahim m.ibrah= im[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 repr= oduce 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 > wro= te: 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 > -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY{=3Dcl.net or u= se:E-mail to administrators: CHEMISTRY-REQUEST{=3Dcl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Feb 6 15:18:01 2010 From: "Reynier Suard az reynier.suardiaz-x-gmail.com" To: CCL Subject: CCL: software to list chi1 angles Message-Id: <-41192-100206134008-29491-azeqOzV7TzBnxumDlm5wGA|,|server.ccl.net> X-Original-From: "Reynier Suard az" Date: Sat, 6 Feb 2010 13:40:05 -0500 Sent to CCL by: "Reynier Suard az" [reynier.suardiaz:+:gmail.com] Dear all I am looking for a free software that be able to list chi1 dihedral angles values of proteins from a pdb file as input. thanks in advance reynier -- _______________________________________________________ Dr. Reynier Suardaz e-mail: reynier(!)fq.uh.cu Dpto.de Qumica Fsica telf.: +53 7 8780684 Facultad de Qumica La Habana, 10400 Universidad de La Habana Cuba url: http://www.fq.uh.cu/investig/gqf/e/lrsdr_en.html _______________________________________________________ From owner-chemistry@ccl.net Sat Feb 6 15:54:00 2010 From: "Mark Onyango mark.onyango.:.tg.fh-giessen.de" To: CCL Subject: CCL: Projection of Inital Guess Orbitals Message-Id: <-41193-100206154239-3993-hfN7HZ/8nwubscc8pMREtA%a%server.ccl.net> X-Original-From: "Mark Onyango" Date: Sat, 6 Feb 2010 15:42:35 -0500 Sent to CCL by: "Mark Onyango" [mark.onyango!^!tg.fh-giessen.de] Good evening everyone, I am trying to conduct a CASSCF calculation using the GAMESS software package on a Mac. I first ran a RHF/STO-3G Singlepoint calculation on an optimized geometry to obtain a set of orbitals. I chose my active space accordingly and reordered the orbitals with NORDER=1 and IORDER. I am now trying to calculate the vertical energies from the groundstate to the first excited state (istate=2) using the cc-pVDZ basis set but keep getting an error concerning the initial guess vectors. My guess is that I am trying to project the guess in a wrong way. Here is my input card: $CONTRL SCFTYP=MCSCF EXETYP=CHECK MAXIT=30 MULT=1 $END $DET NSTATE=6 NELS=10 NACT=9 NCORE=26 IROOT=2 WSTATE(2)=0,1,0,0,0,0 $END $DRT GROUP=CS FORS=.TRUE. $END $MCSCF CISTEP=ALDET $END $SCF DIRSCF=.TRUE. FDIFF=.FALSE. $END $GUESS GUESS=MOREAD NORDER=1 NORB=52 IORDER(23)=27 IORDER(27)=23 $END $SYSTEM TIMLIM=525600 MEMORY=30000000 MEMDDI=1250 PARALL=.TRUE. $END $BASIS GBASIS=CCD $END Any help would be greatly appreciated. Mark Onyango University of applied sciences Giessen, Germany Institute of Biochemical Engeneering and Analytics From owner-chemistry@ccl.net Sat Feb 6 17:13:00 2010 From: "veronica ferraresi veroferraresi]*[gmail.com" To: CCL Subject: CCL:G: G03 Geometry Optimization Fails Message-Id: <-41194-100206161310-12374-6wa79u2VLcK9zYAqAAQsig . server.ccl.net> X-Original-From: veronica ferraresi Content-Type: multipart/alternative; boundary=0016364d2135fac919047ef42961 Date: Sat, 6 Feb 2010 17:10:48 -0300 MIME-Version: 1.0 Sent to CCL by: veronica ferraresi [veroferraresi~!~gmail.com] --0016364d2135fac919047ef42961 Content-Type: text/plain; charset=ISO-8859-1 I'd use scf(xqc) Vero. On 6 February 2010 11:28, 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. > > > --0016364d2135fac919047ef42961 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I'd use scf(xqc)
Vero.

On 6 Februa= ry 2010 11:28,ya= hoo.com <owner-chemistry|-|ccl.net> 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.



--0016364d2135fac919047ef42961-- From owner-chemistry@ccl.net Sat Feb 6 18:18:01 2010 From: "Jamin Krinsky jamink]-[berkeley.edu" To: CCL Subject: CCL:G: G03 Geometry Optimization Fails Message-Id: <-41195-100206165757-5907-sNJ1RYg7iYXabE68OhbORg##server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00c09fa83170ec38cb047ef54938 Date: Sat, 6 Feb 2010 13:31:19 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink_+_berkeley.edu] --00c09fa83170ec38cb047ef54938 Content-Type: text/plain; charset=ISO-8859-1 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 --00c09fa83170ec38cb047ef54938 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Arash,
Almost always when I see "Error termination request pro= cessed 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 i= f this happened. Why the explanation is separate from the actual error mess= age I don't know.
Regards,
Jamin

On Sat, Feb 6, 2010 at = 6:28 AM, *yahoo.co= m <owne= r-chemistry---ccl.net> 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.





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

--00c09fa83170ec38cb047ef54938-- From owner-chemistry@ccl.net Sat Feb 6 21:01:00 2010 From: "Jamin Krinsky jamink(a)berkeley.edu" To: CCL Subject: CCL:G: G09 problem with large-core SD ECP (MWB53 for Gd) Message-Id: <-41196-100206172042-12347-DZuXyjDIq5ZRCSkF9O66hA]|[server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00c09fa21d05628f21047ef5374a Date: Sat, 6 Feb 2010 13:26:08 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink(!)berkeley.edu] --00c09fa21d05628f21047ef5374a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 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 of 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", inst= ead of the default (Harris), when having an odd number of core electrons. Note also that, at each geometry optimization step, the initial 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 each geometry optimization s= tep 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 b= e > > singlet. > > If you run the same job with 3 as charge and 2 as multiplicity, your jo= b > > 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 initi= al > >> 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 script= =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 -> > > --=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 http://glab.cchem.berkeley.edu --00c09fa21d05628f21047ef5374a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 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 of core electrons (why it works with Nd I stil= l don't know. Below is the explanation and work-around proposed by Fern= ando:

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- -c= cl.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.n= et> 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-
>> E-mail to subscribers: CHEMISTRY*ccl.net or use:
>> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= br> >>
>> E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use
>> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message&= gt;> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml>>= =A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt>>
>>
>
>
>
> --
> =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,
> =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 =A0Chemistry Department,
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty of 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.<= br> >
> =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
>



--
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.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST- -ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
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

--00c09fa21d05628f21047ef5374a-- From owner-chemistry@ccl.net Sat Feb 6 23:34:01 2010 From: "maxim totrov max/./molsoft.com" To: CCL Subject: CCL: software to list chi1 angles Message-Id: <-41197-100206212020-19767-JSlL0+tx6/pH6ePuolj3SQ+/-server.ccl.net> X-Original-From: maxim totrov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Sat, 6 Feb 2010 16:54:21 -0800 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: maxim totrov [max*|*molsoft.com] Hi Reynier, you can try our free icm-browser (http://www.molsoft.com/icm_browser.html ), this simple three line script will do what you want: read pdb "1crn" # any pdb code/file convert show Value( v_//xi1 ) Hope this helps Max > > Sent to CCL by: "Reynier Suard az" [reynier.suardiaz:+:gmail.com] > Dear all > I am looking for a free software that be able to list chi1 dihedral > angles values of proteins from a pdb file as input. > thanks in advance > reynier > > > > > -- > _______________________________________________________ > > Dr. Reynier Suardaz e-mail: reynier(-)fq.uh.cu > Dpto.de Qumica Fsica telf.: +53 7 8780684 > Facultad de Qumica La Habana, 10400 > Universidad de La Habana Cuba > url: http://www.fq.uh.cu/investig/gqf/e/lrsdr_en.html > _______________________________________________________ > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/>