From owner-chemistry@ccl.net Mon Feb 11 06:58:00 2013 From: "Bijan Mondal mondal.bijan]_[gmail.com" To: CCL Subject: CCL: Problem with NLMO-NBO calculations. Message-Id: <-48213-130211003215-3918-H5MJy/+Bozhp+DVjStcB4w^server.ccl.net> X-Original-From: Bijan Mondal Content-Type: multipart/alternative; boundary=f46d04451849f27a2404d56c3a38 Date: Mon, 11 Feb 2013 11:02:08 +0530 MIME-Version: 1.0 Sent to CCL by: Bijan Mondal [mondal.bijan- -gmail.com] --f46d04451849f27a2404d56c3a38 Content-Type: text/plain; charset=ISO-8859-1 Dear all, I wanted to calculate bond multiplicity of the compound of my interest. I incorporated pop=NBOread in the route section and putted the following lines after mentioning the basis set. $nbo bndidx nlmo $end I used BP86/def2-SVP basis set. My system contains Ru, C, B, H, O elements and I applied effective core potential on Ru atom. But I am unable to see the result and my calculations ended up with the following lines. NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS: Highest occupied NBOs are not at the beginning of the NBO list; The NLMO program is not currently set up to handle this. Could you please tell me what is the problem and how to solve it? Thank you very much. With best regards, Bijan -- *"There are no such electron-deficient compounds,* * **only theory-deficient chemists." --* R.E. Rundle Bijan Mondal Research Scholar Mob: 7667156593 Department of Chemistry I.I.T Madras Chennai --f46d04451849f27a2404d56c3a38 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear all,
I wanted to calculate bond multiplicity of the compound of my interest= .
I incorporated pop=3DNBOread in the route=20 section and putted the following lines after mentioning the basis set.
$nbo bndidx nlmo $end
I used BP86/def2-SVP basis set. My system contains= Ru, C, B, H, O elements and I applied effective core potential on Ru atom.=

But I am unable to see the result and my calculations ended up with= the following lines.

=A0NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS:

=A0Highe= st occupied NBOs are not at the beginning of the NBO list;
=A0The NLMO p= rogram is not currently set up to handle this.

Could you please tell= me what is the problem and how to solve it?

Thank you very much.
With best regards,
Bijan

"There are no such electron-deficient compounds,<= /span>

=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0 =A0only theory-deficient c= hemists." -- R.E. Rundle

<= font color=3D"#000099"> =A0

Bijan Mondal
Resea= rch Scholar

Mob: 7667156593
Department of Chemistry
I.I.T Madra= s
Chennai

--f46d04451849f27a2404d56c3a38-- From owner-chemistry@ccl.net Mon Feb 11 13:15:00 2013 From: "Daniel Chaves Claudino dclaudino!^!ufl.edu" To: CCL Subject: CCL: DFT/ECP optimization using GAMESS Message-Id: <-48214-130211131401-11516-x4GkV8HXvqmDowXtnTLnQQ!=!server.ccl.net> X-Original-From: "Daniel Chaves Claudino" Date: Mon, 11 Feb 2013 13:14:00 -0500 Sent to CCL by: "Daniel Chaves Claudino" [dclaudino[a]ufl.edu] Hello all, I am trying to run a DFT/ECP (SBKJC) optimization using GAMESS, but it's not working. I've tried different functionals, B3LYP and PBE, but both gave me the same answer. Looking into the output, there were no iterations, the final energy was zero and the following message appears at the end: ***** FAILURE TO LOCATE STATIONARY POINT, SCF HAS NOT CONVERGED with no mention to the number of steps, which is, as far as I know, the common cause for this message to appear. Surprisingly, it seems to work for wavefunction-based methods, since I got an energy minimum for SCF and MP2 methods. Does anyone know how to get it running? Thanks in advance. Daniel From owner-chemistry@ccl.net Mon Feb 11 13:58:01 2013 From: "Mehdi Esrafili m_esrafili.:.yahoo.com" To: CCL Subject: CCL: DFT/ECP optimization using GAMESS Message-Id: <-48215-130211135650-28634-I4XlVJQbMZJ7Fl+7GKJQtg^server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="-83809723-1508665827-1360609003=:74348" Date: Mon, 11 Feb 2013 10:56:43 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili_-_yahoo.com] ---83809723-1508665827-1360609003=:74348 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Daniel;=0AWould you please send me your input file (without atomic coo= rdinates)?=0ARegards=0AMehdi=0A=0A=A0=0A=A0=0A-----------------------------= ---------------------------------------------------------------------------= ----------------------=A0=A0=0A`The man who makes no mistakes does not usua= lly make anything.'=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Edward John Phelps (1822-1= 900)=0A--------------------------------------------------------------------= ---------------------------------------------------------- =0AMehdi D. Esra= fili, Ph.D.=0AAssistant Professor of Physical Chemistry=A0=0ACurrent addres= s:=A0Department of Chemistry, =0AFaculty of Basic Sciences,University of=0A= Maragheh, Iran. =0AE-mail 1:m_esrafili%a%yahoo.com=0AE-mail 2: esrafili%a%marag= heh.ac.ir=0A---------------------------------------------------------------= --------------------------------------------------------------- =0A=0A=0A__= ______________________________=0A From: Daniel Chaves Claudino dclaudino!^!= ufl.edu =0ATo: "Esrafili, Mehdi D " =0ASent: Monday, February 11, 2013 9:44 PM=0ASubject: CCL:= DFT/ECP optimization using GAMESS=0A =0A=0ASent to CCL by: "Daniel Chaves = Claudino" [dclaudino[a]ufl.edu]=0AHello all,=0AI am trying to run a DFT/ECP= (SBKJC) optimization using GAMESS, but it's not =0Aworking. I've tried dif= ferent functionals, B3LYP and PBE, but both gave me the =0Asame answer. Loo= king into the output, there were no iterations, the final =0Aenergy was zer= o and the following message appears at the end:=0A=0A***** FAILURE TO LOCAT= E STATIONARY POINT, SCF HAS NOT CONVERGED=0A=0Awith no mention to the numbe= r of steps, which is, as far as I know, the common =0Acause for this messag= e to appear.=0ASurprisingly, it seems to work for wavefunction-based method= s, since I got an =0Aenergy minimum for SCF and MP2 methods. =0ADoes anyone= know how to get it running?=0AThanks in advance.=0A=0ADaniel=0A=0A=0A=0A-= =3D This is automatically added to each message by the mailing script =3D-= =0A= =0A=0Aloo= k up the X-Original-From: line in the mail header.=0A=0AE-mail to subscribe= rs: CHEMISTRY%a%ccl.net or use:=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/= send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST%a%ccl.net o= r use=0A=A0 =A0 =A0=0A=0ASu= bscribe/Unsubscribe: =0A=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.= shtml=0A=0A=0A=0AJob:= http://www.ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/an= nouncements/conferences/=0A=0ASearch Messages: http://www.ccl.net/chemistry= /searchccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.7.1 error,= check:=0A=A0 =A0 =A0=0A=0ARTFI: http://www= .ccl.net/chemistry/aboutccl/instructions/ ---83809723-1508665827-1360609003=:74348 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Daniel;

Would you please send me your input file (with= out atomic coordinates)?

Regards

Mehdi

---------------------------------------------------------------= --------------------------------------------------------------- =

`The man who makes no mistakes does not usually make anything.'

&n= bsp; = ; Edward John Phelps = (1822-1900)

-------------------------------------------------------= ----------------------------------------------------------------------- Mehdi D. Esrafili, Ph.D.

Assistant Professor of Physical Chemistry
Current address: Department of Chemistry, <= /font>

Faculty of Basic Sciences,University of

Maragheh, Iran.

E-mail 1: m_e= srafili%a%yahoo.com
E-mail 2: esrafili%a%maragheh.ac.ir

-------------------------------------------------= ---------------------------------------------------------------------------= --

From: Daniel Chaves Claudino dclaudino!^!ufl.= edu <owner-chemistry%a%ccl.net>
To: "Esrafili, Mehdi D " <m_esrafili%a%yahoo.com>=
Sent: Monday, Februa= ry 11, 2013 9:44 PM
Subject: CCL: DFT/ECP optimization using GAMESS

=0ASent to CCL by: "Daniel Chaves Claudino" [dclaudino[a]ufl.edu]
Hello all,
I am trying to run = a DFT/ECP (SBKJC) optimization using GAMESS, but it's not
working. I've= tried different functionals, B3LYP and PBE, but both gave me the
same = answer. Looking into the output, there were no iterations, the final
en= ergy was zero and the following message appears at the end:

***** FA= ILURE TO LOCATE STATIONARY POINT, SCF HAS NOT CONVERGED

with no ment= ion to the number of steps, which is, as far as I know, the common
caus= e for this message to appear.
Surprisingly, it seems to work for wavefun= ction-based methods, since I got an
energy minimum for SCF and MP2 meth= ods.
Does anyone know how to get it running?
Thanks in advance.
<= br>Daniel

-=3D This is automatically added to each message b= y the mailing script =3D-the strange characters on the top line to= the %a% sign. You can also
look up the X-Original-From: line in the mail = header.

E-mail to subscribers: CHEMISTRY%a%ccl.net or use:
= ;

E-ma= il to administrators: CHEMISTRY-REQUEST%a%ccl.net or use<= br> http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /a>
http://www.ccl.n= et/chemistry/sub_unsub.shtml

Before posting, check wait time at: htt= p://www.ccl.net
Conferences: http:/= /server.ccl.net/chemistry/announcements/conferences/

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

If your mail bou= nces from CCL with 5.7.1 error, check:
http://www.c= cl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/inst= ructions/

okman old style, new york, times, serif;font-size:14pt">

Dear pan>Daniel;

ont-family: bookman old style,new york,times,serif; background-color: trans= > parent; font-style: normal;">Would you please send me your input file (with= > out atomic coordinates)?

18.6667px; font-family: bookman old style,new york,times,serif; background= > -color: transparent; font-style: normal;">Regards

rgb(0, 0, 0); font-size: 18.6667px; font-family: bookman old style,new yor= > k,times,serif; background-color: transparent; font-style: normal;">Mehdi >

, new york, times, serif" > size=3D"4">---------------------------------------------------------------= > --------------------------------------------------------------- = >

ze=3D"4">`The man who makes no mistakes does not usually make anything.' ont>

=3D"4"> &n= > bsp; = > ; Edward John Phelps = > (1822-1900)

, serif" size=3D"4">-------------------------------------------------------= > ----------------------------------------------------------------------- >Mehdi D. Esrafili, Ph.D.

ew york, times, serif" size=3D"4">Assistant Professor of Physical > Chemistry
Current address: Department of Chemistry, <= > /font>

e=3D"4">Faculty of Basic Sciences,University of

=3D"times new roman, new york, times, serif" size=3D"4">Maragheh, Iran. ont>

=3D"4">E-mail 1: m_e= > srafili%a%yahoo.com
E-mail 2: t> c.ir"> if" size=3D"4">esrafili%a%maragheh.ac.ir

rial, helvetica, sans-serif"> , new york, times, serif">-------------------------------------------------= > ---------------------------------------------------------------------------= > -- >

d style, new york, times, serif; font-size: 14pt;">

ly: times new roman, new york, times, serif; font-size: 12pt;">

"ltr">

font-weight:bold;">From: Daniel Chaves Claudino dclaudino!^!ufl.= > edu <owner-chemistry%a%ccl.net>
;">To: "Esrafili, Mehdi D " <m_esrafili%a%yahoo.com>= >
Sent: Monday, Februa= > ry 11, 2013 9:44 PM
Subject: n> CCL: DFT/ECP optimization using GAMESS

=0A >Sent to CCL by: "Daniel Chaves Claudino" [dclaudino[a] href=3D"http://ufl.edu/">ufl.edu]
Hello all,
I am trying to run = > a DFT/ECP (SBKJC) optimization using GAMESS, but it's not
working. I've= > tried different functionals, B3LYP and PBE, but both gave me the
same = > answer. Looking into the output, there were no iterations, the final
en= > ergy was zero and the following message appears at the end:

***** FA= > ILURE TO LOCATE STATIONARY POINT, SCF HAS NOT CONVERGED

with no ment= > ion to the number of steps, which is, as far as I know, the common
caus= > e for this message to appear.
Surprisingly, it seems to work for wavefun= > ction-based methods, since I got an
energy minimum for SCF and MP2 meth= > ods.
Does anyone know how to get it running?
Thanks in advance.
<= > br>Daniel

-=3D This is automatically added to each message b= > y the mailing script =3D-the strange characters on the top line to= > the %a% sign. You can also
look up the X-Original-From: line in the mail = > header.

E-mail to subscribers: t" href=3D"mailto:CHEMISTRY%a%ccl.net">CHEMISTRY%a%ccl.net or use:
= > ;

E-ma= > il to administrators: =3D"mailto:CHEMISTRY-REQUEST%a%ccl.net">CHEMISTRY-REQUEST%a%ccl.net or use<= > br> message" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= > /a>
http://www.ccl.n= > et/chemistry/sub_unsub.shtml

Before posting, check wait time at: htt= > p://www.ccl.net
Conferences: http:/= > /server.ccl.net/chemistry/announcements/conferences/

Search Messages= > : > http://www.ccl.net/chemistry/searchccl/index.shtml

If your mail bou= > nces from CCL with 5.7.1 error, check:
http://www.c= > cl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/inst= > ructions/

> ---83809723-1508665827-1360609003=:74348-- > > From owner-chemistry@ccl.net Mon Feb 11 18:31:00 2013 From: "Joy Ku joyku|-|stanford.edu" To: CCL Subject: CCL: Workshop: Rapid Molecular Dynamics Prototyping & Simulations on GPUs Message-Id: <-48218-130211182747-23746-xhdP57q31p9kbvtldzQ46Q#server.ccl.net> X-Original-From: "Joy Ku" Date: Mon, 11 Feb 2013 18:27:45 -0500 Sent to CCL by: "Joy Ku" [joyku##stanford.edu] Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. Where: Stanford University When: March 26-29, 2013 Registration: Free but required and spaces are limited. To register or for more information, visit http://simbios.stanford.edu/MDWorkshop.htm. OpenMM (http://simtk.org/home/openmm) is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs). Its performance, openness, and extreme flexibility via custom forces and integrators make it truly unique among simulation codes. A well-designed framework provides an application layer and a library, so that non-programmers can easily and quickly run MD simulations and develop custom algorithms on GPUs, while programmers are simultaneously able to integrate OpenMM cleanly into their own programs. The workshop offers two tracks: one for those who want to use OpenMM to run molecular dynamics simulations (no programming experience is needed), and another for programmers interested in integrating OpenMM into their own software. The last two days of the workshop are devoted to having the OpenMM team assist participants with their individual projects. You can sign up for an instructional track, just the open working days, or both. ________________________________________ OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. [2]Eastman, P. and Pande, V.S., Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit, J. Comp. Chem., 2010, 31(6):1268-1272. From owner-chemistry@ccl.net Mon Feb 11 21:59:00 2013 From: "Pieremanuele C. canepap : wfu.edu" To: CCL Subject: CCL:G: Use a MP2 checkpoint as a starting point for a DFT calculation Message-Id: <-48219-130211205705-9675-V61husxkRmr2WU+S+BTKFg[A]server.ccl.net> X-Original-From: "Pieremanuele C." Content-Type: multipart/alternative; boundary="Apple-Mail=_E44F0B76-A0AC-43D6-AAFD-B9B12BF7F134" Date: Mon, 11 Feb 2013 20:56:59 -0500 Mime-Version: 1.0 (Mac OS X Mail 6.2 $1499$) Sent to CCL by: "Pieremanuele C." [canepap%a%wfu.edu] --Apple-Mail=_E44F0B76-A0AC-43D6-AAFD-B9B12BF7F134 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear All,=20 The questions I'm about to ask are very silly, I know. In our lab we are = doing some experiments with our vDW-DF functional we are currently using = to take into account Van der Waals Interactions in solids.=20 However, my first question is: I'd like to use as a restart for a DFT = calculation a MP2 or CC density as produced by Gaussian, is that = possible?=20 Say I have run my MP2 job and I saved the checkpoint, which includes = the accurate MP2 wave function, integrals, geometry etc., but also the = accurate MP2 density; now is it possible to use this checkpoint to start = DFT calculation ?=20 Below I report the first part of my Gaussian09 input that I have gotten = to work, however I'm not sure that the DFT is really using the MP2 = density as a starting point. Can you clarify it=20 %chk=3Dmp2.chk <----- checkpoint from MP2job=20 %mem=3D8GB %NProcShared=3D8 #SP PBEPBE/6-311++G(d,p) SCF=3D(MaxConventionalCycles=3D2) Guess=3DRead = fchk=20 Second question: it's is possible to have Gaussian to print all the = Energy contribution to the Total energy? Say N-N, N-E and KE ?=20 Third question: how can I make the output very verbose ?=20 Thanks, Piero=20 ______________________________________ Pieremanuele (Piero) Canepa PhD Wake Forest University, Department of Physics Winston-Salem, NC 27109 (USA) t: +001 (336) 758 4222 c: +001 (336) 602 6045 f: +001 (336) 758 6142 Skype: pieremanuele=20 --Apple-Mail=_E44F0B76-A0AC-43D6-AAFD-B9B12BF7F134 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Dear = All,

The questions I'm about to ask are very = silly, I know. In our lab we are doing some experiments with our = vDW-DF functional we are currently using to take into account Van = der Waals Interactions in = solids.

However, my = first question is: I'd like to use as a restart for a DFT = calculation a MP2 or CC density as produced by Gaussian, is that = possible?

Say I have run my MP2 job and I = saved the checkpoint, which includes the accurate MP2 wave = function, integrals, geometry etc., but also the accurate MP2 = density; now is it possible to use this checkpoint to start DFT = calculation ?

Below I report the first = part of my Gaussian09 input that I have gotten to work, however = I'm not sure that the DFT is really using the MP2 density as a = starting point. Can you clarify = it

%chk=3Dmp2.chk <----- = checkpoint from = MP2job

%mem=3D8GB

%NProcShared=3D8

#SP= PBEPBE/6-311++G(d,p) SCF=3D(MaxConventionalCycles=3D2) Guess=3DRead= fchk

Second question: = it's is possible to have Gaussian to print all the Energy contribution = to the Total energy? Say N-N, N-E and KE = ?

Third question: how can I make = the output very verbose ?

Thanks, = Piero

______________________________________

Pie= remanuele (Piero) Canepa PhD

Wake Forest University, Department = of Physics
Winston-Salem, NC 27109 (USA)
t: +001 (336) 758 = 4222
c: +001 (336) 602 6045
f: +001 (336) 758 6142
Skype: = pieremanuele

= --Apple-Mail=_E44F0B76-A0AC-43D6-AAFD-B9B12BF7F134--