From owner-chemistry@ccl.net Fri Mar 22 09:21:00 2013 From: "Christo Z Christov christo.christov###northumbria.ac.uk" To: CCL Subject: CCL: invitation for contributions "Computational Molecular Bioscience" Message-Id: <-48450-130322012431-20361-69JaSWERz465ZJqLNQzF7g_+_server.ccl.net> X-Original-From: "Christo Z Christov" Date: Fri, 22 Mar 2013 01:24:30 -0400 Sent to CCL by: "Christo Z Christov" [christo.christov^-^northumbria.ac.uk] Dear Colleagues, I would like to invite you to contribute with publication to our journal "Computational Molecular Bioscience" http://www.scirp.org/journal/cmb. We founded CMB in the fall of 2011 and our vision and focus is on consistent increase of the quality and impact of publications we accept. In order to support outstanding and excellent contributions we might consider discount from the publication fees. All areas of computational molecular and biomolecular science, both method developments and applications will be very welcome as well combined computational and experimental studies and applications of computational modelling in applied and innovative research. With best regards, Dr Christo Z Christov Editor in Chief and Founder Computational Molecular Bioscience http://www.scirp.org/journal/cmb/ Senior Lecturer in Computational Biochemistry, Department of Applied Sciences, School of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK http://www.northumbria.ac.uk/sd/academic/lifesciences/ad/biomed/staff/cchristov/ From owner-chemistry@ccl.net Fri Mar 22 09:56:00 2013 From: "Meilani Kurniawati Wibowo piano_oz1989() yahoo.co.id" To: CCL Subject: CCL:G: NBO - Bond Order Message-Id: <-48451-130322041334-5182-Y8WHN/81gFPd8rEtlt5FkA%a%server.ccl.net> X-Original-From: "Meilani Kurniawati Wibowo" Date: Fri, 22 Mar 2013 04:13:27 -0400 Sent to CCL by: "Meilani Kurniawati Wibowo" [piano_oz1989_+_yahoo.co.id] Dear all, How to determine the bond order from the Gaussian output file? What keyword I have to add to get the value of bond order? Thank you. From owner-chemistry@ccl.net Fri Mar 22 10:31:00 2013 From: "=?UTF-8?Q?Serdar_Bado=C4=9Flu?= serdarbadoglu{=}gmail.com" To: CCL Subject: CCL:G: DFT and MP2 Message-Id: <-48452-130322083025-1309-mECEtd1PPRgNec1/1COwSQ ~ server.ccl.net> X-Original-From: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= Content-Type: multipart/alternative; boundary=14dae9340e3b3d183f04d8829ebd Date: Fri, 22 Mar 2013 14:30:18 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= [serdarbadoglu]^[gmail.com] --14dae9340e3b3d183f04d8829ebd Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable At the moment MP2/6-311++G** give no errors if the calculation is only optimization. If it's freq or opt+freq it gives error again. I have tried to determine the memory requirement for my calculation. From a brief search I could find that I should use either 3N^2 or M+2N^2 words of memory. M is the minimum default memory for Gaussian (which is 256 megabytes). N is the number of basis functions. According to my unfinished Gaussian calculations, N is 275 for my molecule. So, if I correctly understand I need at least 256 megabytes plus some 150 kilowords, which is totally less than 300 megabytes of memory. I have 12 gigabytes of physical memory and my %mem setting was 1 gigabytes per core. So, I couldn't understand how my problem has been turned out to be a memory issue. Meanwhile, with help of a colleague I have reached an HPCC. I start to calculate my molecule at MP2/6-311++G** level, opt + freq, %mem=3D4GB, %nprocshared=3D4. It ended successfully. So, what's wrong with me? On Fri, Mar 15, 2013 at 9:37 PM, Abrash, Sam sabrash#%#richmond.edu < owner-chemistry]|[ccl.net> wrote: > Before you give up increase %mem to %mem=3D10GB or whatever the largest > your computer will allow.**** > > ** ** > > Samuel A. Abrash > Department of Chemistry**** > > Coordinator, Environmental Studies Progrram > University of Richmond > Richmond, VA 23173 > Phone (Gottwald): 804-289-8248**** > > Phone (International Center): 804-484-1473 > Fax: 804-287-1897 > E-mail: sabrash]|[richmond.edu > Web-page: http://www.richmond.edu/~sabrash > **** > > "That's one of the tragedies of this life, that the men who are most in > need of a beating are always enormous." Rudy Valee, as J. D. Hackensacker= , > III, in the Preston Sturges Film "The Palm Beach Story"**** > > ** ** > > *From:* owner-chemistry+sabrash=3D=3Drichmond.edu]|[ccl.net [mailto: > owner-chemistry+sabrash=3D=3Drichmond.edu]|[ccl.net] *On Behalf Of *Serdar > Badoglu serdarbadoglu!A!gmail.com > *Sent:* Friday, March 15, 2013 1:24 PM > *To:* Abrash, Sam > *Subject:* CCL:G: DFT and MP2**** > > ** ** > > ** ** > > 6-31G* worked. I have observed that I get error when I add diffuse > functions on heavy atoms. But I need them. I was aimed to do my > calculations with 6-311++G** basis set, because that was the set I have > used in my DFT calculations and I want to see the difference between both > methods. I'll try to reach that level by increasing the polarity and > diffuse functions step by step until I reach the limits of my pc.**** > > ** ** > > Thank you all.**** > > ** ** > > On Fri, Mar 15, 2013 at 10:31 AM, Stephan Ehrlich stephan.ehrlich]_[ > uni-muenster.de wrote:**** > > > Sent to CCL by: "Stephan Ehrlich" [stephan.ehrlich],[uni-muenster.de] > Dear Serdar, > > while it apparently solves your technical problem, I would strongly > discourage > you from trusting the results of an MP2/3-21g calculation. The basis is > much > too small and does not account for correlation properly. > It also completely lacks polarization functions. Using it will lead to > large basis set > superposition and incompleteness errors (BSSE and BSIE). > I would suggest a basis set of at least triple-zeta quality, with > polarization > functions (and augmented with diffuse functions when you are looking at > non-covalent > interactions). As an example, the correlation-consistent basis sets by > Dunning and co-workers > (e.g. cc-pVTZ and aug-cc-pVTZ in this case) fulfill these criteria. I am > no Gaussian expert, > but sure that they are implemented in Gaussian. > > Cheers and good luck, > > Stephan.**** > > > > > On Fri, 15 Mar 2013 02:53:00 +0100, Serdar Bado=C4=9Flu serdarbadoglu() > gmail.com wrote:**** > > I haven't seen such a message. > > Finally there's hope for me. I have changed the command line as # opt fre= q > mp2/3-21g geom=3Dconnectivity, memory settings stayed the same. Finished > successfully in 20 minutes.**** > > ** ** > > ____________________________________________________________ > Stephan Ehrlich (stephan.ehrlich__thch.uni-bonn.de) > Mulliken Center for Theoretical Chemistry > Institut fuer Physikalische und Theoretische Chemie > Universitaet Bonn, Beringstr. 4, D-53115 Bonn, Germany > ____________________________________________________________**** > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-
> > E-mail to subscribers: CHEMISTRY[A]ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST[A]ccl.net or use**** > > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/****>
> **** > > > > **** > > ** ** > > -- > Serdar BADO=C4=9ELU, Ph.D. > Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm=C3=BC**** > --=20 Serdar BADO=C4=9ELU, Ph.D. Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm=C3=BC --14dae9340e3b3d183f04d8829ebd Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
At the moment MP2/6-311++G** give no errors if the calculation is only= optimization. If it's freq or opt+freq it gives error again.

I have tried to determine the memory requirement for my cal= culation. From a brief search I could find that I should use either 3N^2 or= M+2N^2 words of memory. M is the minimum default memory for Gaussian (whic= h is 256 megabytes). N is the number of basis functions.

According to my unfinished Gaussian calculations, N is = 275 for my molecule. So, if I correctly understand I need at least 256 mega= bytes plus some 150 kilowords, which is totally less than 300 megabytes of = memory. I have 12 gigabytes of physical memory and my %mem setting was 1 gi= gabytes per core. So, I couldn't understand how my problem has been tur= ned out to be a memory issue.

Meanwhile, with help of a colleague I have reached an H= PCC. I start to calculate my molecule at MP2/6-311++G** level, opt + freq, = %mem=3D4GB, %nprocshared=3D4. It ended successfully.

So, what's wrong with me?


On Fri, Mar 15, 2013 at 9:37 PM, Abrash, Sam sabrash#%#richmond.edu <owner-chemistry]|[ccl.net><= /span> wrote:

Before you give up increa= se %mem to %mem=3D10GB or whatever the largest your computer will allow.=

=C2=A0

Samuel A. Abrash
Department of Chemistry

Coordinator, Environmenta= l Studies Progrram
University of Richmond
Richmond, VA 23173
Phone (Gottwald):=C2=A0 804-289-8248

Phone (International Cent= er): = 804-484-1473
Fax:=C2=A0 804-287-1897
E-mail:=C2=A0 sab= rash]|[richmond.edu
Web-page:=C2=A0 http://www.richmond.edu/~sabrash

"That's one of t= he tragedies of this life, that the men who are most in need of a beating a= re always enormous." Rudy Valee, as J. D. Hackensacker, III, in the Pr= eston Sturges Film "The Palm Beach Story"

=C2=A0

From: owner-ch= emistry+sabrash=3D=3Drichmond.edu]|[ccl.net [mailto:owner-chemistry+sabrash=3D=3Drichmond.edu]|[ccl.net] On Behalf Of Serdar Badoglu serdarbadoglu!A!gmail.com
Sent: Friday, March 15, 2013 1:24 PM
To: Abrash, Sam
Subject: CCL:G: DFT and MP2

=C2=A0

=C2=A0

6-31G* worked. I have observed that I get error when= I add diffuse functions on heavy atoms. But I need them. I was aimed to do= my calculations with 6-311++G** basis set, because that was the set I have= used in my DFT calculations and I want to see the difference between both methods. I'll try to reach tha= t level by increasing the polarity and diffuse functions step by step until= I reach the limits of my pc.

=C2=A0

Thank you all.

=C2=A0<= /p>

On Fri, Mar 15, 2013 at 10:31 AM, Stephan Ehrlich st= ephan.ehrlich]_[uni-mu= enster.de <owner-chemistry[A]ccl.net> wrote:


Sent to CCL by: "Stephan Ehrlich" [stephan.ehrlich],[uni-muenster.de]
Dear Serdar,

while it apparently solves your technical problem, I would strongly discour= age
you from trusting the results of an MP2/3-21g calculation. The basis is muc= h
too small and does not account for correlation properly.
It also completely lacks polarization functions. Using it will lead to larg= e basis set
superposition and incompleteness errors (BSSE and BSIE).
I would suggest a basis set of at least triple-zeta quality, with polarizat= ion
functions (and augmented with diffuse functions when you are looking at non= -covalent
interactions). As an example, the correlation-consistent basis sets by Dunn= ing and co-workers
(e.g. cc-pVTZ and aug-cc-pVTZ in this case) fulfill these criteria. I am no= Gaussian expert,
but sure that they are implemented in Gaussian.

Cheers and good luck,

Stephan.




On Fri, 15 Mar 2013 02:53:00 +0100, Serdar Bado=C4=9Flu serdarbadoglu()
gmail.com <owner-chemistry__ccl.ne= t> wrote:

I haven't seen such a message.

Finally there's hope for me. I have changed the command line as # opt f= req
mp2/3-21g geom=3Dconnectivity, memory settings stayed the same. Finished successfully in 20 minutes.

=C2=A0

____________________________________________________= ________
Stephan Ehrlich (stephan.ehrlich__thch.uni-bonn.de)
Mulliken Center for Theoretical Chemistry
Institut fuer Physikalische und Theoretische Chemie
Universitaet Bonn, Beringstr. 4, D-53115 Bonn, Germany
____________________________________________________________<= /p>





-=3D This is automatically added to each message by the mailing script =3D-= <br


E-mail to subscribers: CHEMISTRY[A]ccl.net or use:
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E-mail to administrators: CHEMISTRY-REQUEST[A]ccl.net or use
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= br> =

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

Job: http://www.ccl.net/jobsConferences: http://server.ccl.net/chemistry/announcements/conferences/



=C2=A0

--
Serdar BADO=C4=9ELU, Ph.D.
Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm=C3=BC




--
Serdar BADO= =C4=9ELU, Ph.D.
Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm=C3=BC
--14dae9340e3b3d183f04d8829ebd-- From owner-chemistry@ccl.net Fri Mar 22 11:48:00 2013 From: "Sergio Galembeck segalemb[]usp.br" To: CCL Subject: CCL:G: NBO - Bond Order Message-Id: <-48453-130322101953-5468-qb1yJAWj7Rhgb94hGf3L3w*|*server.ccl.net> X-Original-From: Sergio Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 22 Mar 2013 11:19:37 -0300 Mime-Version: 1.0 (Mac OS X Mail 6.3 \(1503\)) Sent to CCL by: Sergio Galembeck [segalemb{:}usp.br] Dear Melani, if you have NBO 3.1, that comes with Gxx, you need to use pop=nboread keyword and after the geometry and a blank line, put a line with: $nbo bndidx $end. After, add a blank line. Best regards, Sergio On 22/03/2013, at 05:13, "Meilani Kurniawati Wibowo piano_oz1989() yahoo.co.id" wrote: > > Sent to CCL by: "Meilani Kurniawati Wibowo" [piano_oz1989_+_yahoo.co.id] > Dear all, > > How to determine the bond order from the Gaussian output file? What keyword I > have to add to get the value of bond order? > > Thank you.> > From owner-chemistry@ccl.net Fri Mar 22 12:23:00 2013 From: "Chang, Christopher Christopher.Chang%%nrel.gov" To: CCL Subject: CCL:G: NBO - Bond Order Message-Id: <-48454-130322115910-16197-bIRb1jAh3xeH9yK847HGVA##server.ccl.net> X-Original-From: "Chang, Christopher" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 22 Mar 2013 09:58:55 -0600 MIME-Version: 1.0 Sent to CCL by: "Chang, Christopher" [Christopher.Chang^^^nrel.gov] In Gaussian route: Pop=NBORead At bottom of input file (usually .com or .gjf extensions): $NBO NBO BNDIDX $END This should produce Coulson ("MO bond orders"), Wiberg, and atom-atom overlap weighted NAO bond orders. If you want the "NLMO/NPA" bond orders, the NBO line should contain the NLMO keyword as well, like: $NBO NBO NLMO BNDIDX $END With NBORead, the Gaussian input deck should NOT be blank-line terminated as is usual. So, the last line in the file should be the $NBO... text The above works with NBO 5 and up; the standard Gaussian distribution includes only NBO 3.1, so YMMV with the above. NLMOs are available from Gaussian, so I think it should work. -----Original Message----- > From: owner-chemistry+christopher.chang==nrel.gov!A!ccl.net [mailto:owner-chemistry+christopher.chang==nrel.gov!A!ccl.net] On Behalf Of Meilani Kurniawati Wibowo piano_oz1989() yahoo.co.id Sent: Friday, March 22, 2013 2:13 AM To: Chang, Christopher Subject: CCL:G: NBO - Bond Order Sent to CCL by: "Meilani Kurniawati Wibowo" [piano_oz1989_+_yahoo.co.id] Dear all, How to determine the bond order from the Gaussian output file? What keyword I have to add to get the value of bond order? Thank you.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Mar 22 12:58:00 2013 From: "Raphael Martinez raphaelmartinez1983() gmail.com" To: CCL Subject: CCL:G: Redundant coordinates Message-Id: <-48455-130322122003-25579-d3jRwebDKMPwr3DYJMgDWQ]_[server.ccl.net> X-Original-From: "Raphael Martinez" Date: Fri, 22 Mar 2013 12:20:01 -0400 Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983~~gmail.com] Hello everyone, I try to find this information in the Gaussian manual or in google, but I could not find it. I am using gaussian 09. In te Redundant options, what is the difference between "Add" and "Build" a coordinate? Although I am just interested on "add" and "build", It would be nice if someone also tell me what is the "Hessian" and "derivative" options for....thanks for the help From owner-chemistry@ccl.net Fri Mar 22 13:47:00 2013 From: "mehedi mehedi.acct^-^gmail.com" To: CCL Subject: CCL: Crystal Structure Message-Id: <-48456-130322134558-6470-CPs6KNOvXEDWisFN5m7rVA\a/server.ccl.net> X-Original-From: mehedi Content-Type: multipart/alternative; boundary=047d7bd9161eca49b604d8870624 Date: Fri, 22 Mar 2013 12:45:52 -0500 MIME-Version: 1.0 Sent to CCL by: mehedi [mehedi.acct-.-gmail.com] --047d7bd9161eca49b604d8870624 Content-Type: text/plain; charset=ISO-8859-1 thanks, I'll give a try on that --047d7bd9161eca49b604d8870624 Content-Type: text/html; charset=ISO-8859-1 thanks, I'll give a try on that --047d7bd9161eca49b604d8870624-- From owner-chemistry@ccl.net Fri Mar 22 14:31:00 2013 From: "Thomas Manz thomasamanz]*[gmail.com" To: CCL Subject: CCL:G: NBO - Bond Order Message-Id: <-48457-130322122826-7137-bCIx+G3ltLy1bhp6NBoEIA*_*server.ccl.net> X-Original-From: Thomas Manz Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 22 Mar 2013 10:28:20 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz^^gmail.com] Dear Meilani Kurniawati Wibowo, I recommend the spin-corrected Mayer bond order in the NAO basis, which is accurate and reliable for molecular systems. The spin-corrected Mayer bond order is defined by Equation (11) of the article I. Mayer, "On Bond Orders and Valences in the Ab Initio Quantum Chemical Theory," Int. J. Quant. Chem. Vol. 29, (1986) pp. 73-84. This equation is reproduced as Equations (44) and (46) of the review article I. Mayer, "Bond Order and Valence Indices: A Personal Account," J. Comput. Chem. Vol. 28 (2007) pp. 204-221. Mayer applied his definition using the basis set (Mulliken analysis) to compute the overlap matrix, but this leads to high basis set sensitivity. The problem of high basis set sensitivity in Mulliken analysis was resolved by Natural Population Analysis which generates Natural Atomic Orbitals (NAOs) as described in the article A.E. Reed, R.B. Weinstock, and F. Weinhold, "Natural population analysis," J. Chem. Phys. Vol. 83 (1985) pp. 735-746. The spin-corrected Mayer bond order in the NAO basis uses Natural Population Analysis to compute the overlap matrices. It can be computed as following: 1) add Pop=NBOread to the route line of the Gaussian input file 2) add the following line to the bottom of file: $NBO BNDIDX RESONANCE $END (One blank line should occur before and after this line.) 3) After the jobs completes, search the Gaussian output file for the line "Wiberg bond index matrix in the NAO basis:". Depending on the type of job, this line may occur multiple times in the log file, so you must be careful to identify the right ones. By default, Gaussian performs population analysis on the first and last steps of a geometry optimization. You want to use the entry for the last geometry step, which will appear near the bottom of the output file. If the geometry does not change during the calculation (e.g., single-point or frequency calculation), then the population analysis will be performed only once (unless you have requested a multi-part job). For spin unpolarized systems: The spin-corrected Mayer bond order in the NAO basis equals the "Wiberg bond index in the NAO basis" so you can just read the corresponding entry from the Gaussian output file. (Do not multiply by two.) For spin polarized systems: The spin-corrected Mayer bond order in the NAO basis = 2*W(alpha) + 2*W(beta), where W(alpha) is the Wiberg bond index in the NAO basis for the alpha spin orbitals and W(beta) is the Wiberg bond index in the NAO basis for the beta spin orbitals. For spin polarized systems NBO analysis is automatically performed three times: first for the total density matrix (ignore this part) then for the spin up (alpha) density matrix in the section following the lines *************************************************** ******* Alpha spin orbitals ******* *************************************************** W(alpha) is the entry under "Wiberg bond index matrix in the NAO basis:" and finally for the spin down (beta) density matrix in the section following the lines *************************************************** ******* Beta spin orbitals ******* *************************************************** W(beta) is the entry under "Wiberg bond index matrix in the NAO basis:" Example: The O2 molecule. Since the ground state of the O2 molecule is a spin triplet, this is a spin polarized calculation. Below is an excerpt of lines from the Gaussian output file: *************************************************** ******* Alpha spin orbitals ******* *************************************************** (deleted lines) Wiberg bond index matrix in the NAO basis: Atom 1 2 ---- ------ ------ 1. O 0.0000 0.2560 2. O 0.2560 0.0000 (more deleted lines) *************************************************** ******* Beta spin orbitals ******* *************************************************** (deleted lines) Wiberg bond index matrix in the NAO basis: Atom 1 2 ---- ------ ------ 1. O 0.0000 0.7505 2. O 0.7505 0.0000 (more delete lines) So, the effective bond order for the O2 molecule is: 2*0.2560 + 2*0.7505 = 2.013. (Note: The Wiberg bond index is symmetric, so you can look for either the entry (1,2) or the entry (2,1) to get the terms for the bond between atom 1 and atom 2.) In my experience, this is one of the most reliable ways to compute effective bond orders of molecular systems. Sincerely, Tom Manz On Fri, Mar 22, 2013 at 2:13 AM, Meilani Kurniawati Wibowo piano_oz1989() yahoo.co.id wrote: > > Sent to CCL by: "Meilani Kurniawati Wibowo" [piano_oz1989_+_yahoo.co.id] > Dear all, > > How to determine the bond order from the Gaussian output file? What keyword I > have to add to get the value of bond order? > > Thank you.> > From owner-chemistry@ccl.net Fri Mar 22 15:06:01 2013 From: "Daniel Jana dfjana{=}gmail.com" To: CCL Subject: CCL:G: DFT and MP2 Message-Id: <-48458-130322123333-11443-lK1R9itUpYQ0Xlp0zmRu6Q a server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 22 Mar 2013 17:33:26 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana^^gmail.com] Hello, So you basically ran one computation with 1GB of RAM and another with 4 GB of RAM and are wondering why one finishes and the other one doesn't? The value you give in %Mem is a shared memory value. Yes, you are running it in 4 CPU, but it's not like each CPU is limited to 1 GB. The entire 4 GB are common to the set of 4 CPU. So, in one case your job doesn't finish because (for frequencies) 1 GB seems not to be enough. In the other case, it does finish because 4 GB is enough. Unless you are trying to run several computations at the same time, I don't see why are you "afraid" of using those 12 GB. The values suggested by these simple formulas available in Gaussian's website are the minimal value the job can use, but they don't mean you can't use more. In case you are indeed limiting the amount of RAM you are using indeed because you want to run multiple jobs in the same machine, keep in mind that the scratch usage may be your limiting factor. If you have several jobs trying to write (or read) simultaneously from the same hard drive, it doesn't matter how many cores and GB of RAM you have... your jobs will slow down to a halt. Best, Daniel On 22 March 2013 13:30, Serdar Badoğlu serdarbadoglu{=}gmail.com wrote: > At the moment MP2/6-311++G** give no errors if the calculation is only > optimization. If it's freq or opt+freq it gives error again. > > I have tried to determine the memory requirement for my calculation. From a > brief search I could find that I should use either 3N^2 or M+2N^2 words of > memory. M is the minimum default memory for Gaussian (which is 256 > megabytes). N is the number of basis functions. > > According to my unfinished Gaussian calculations, N is 275 for my molecule. > So, if I correctly understand I need at least 256 megabytes plus some 150 > kilowords, which is totally less than 300 megabytes of memory. I have 12 > gigabytes of physical memory and my %mem setting was 1 gigabytes per core. > So, I couldn't understand how my problem has been turned out to be a memory > issue. > > Meanwhile, with help of a colleague I have reached an HPCC. I start to > calculate my molecule at MP2/6-311++G** level, opt + freq, %mem=4GB, > %nprocshared=4. It ended successfully. > > So, what's wrong with me? > > > On Fri, Mar 15, 2013 at 9:37 PM, Abrash, Sam sabrash#%#richmond.edu > wrote: >> >> Before you give up increase %mem to %mem=10GB or whatever the largest your >> computer will allow. >> >> >> >> Samuel A. Abrash >> Department of Chemistry >> >> Coordinator, Environmental Studies Progrram >> University of Richmond >> Richmond, VA 23173 >> Phone (Gottwald): 804-289-8248 >> >> Phone (International Center): 804-484-1473 >> Fax: 804-287-1897 >> E-mail: sabrash[*]richmond.edu >> Web-page: http://www.richmond.edu/~sabrash >> >> "That's one of the tragedies of this life, that the men who are most in >> need of a beating are always enormous." Rudy Valee, as J. D. Hackensacker, >> III, in the Preston Sturges Film "The Palm Beach Story" >> >> >> >> From: owner-chemistry+sabrash==richmond.edu[*]ccl.net >> [mailto:owner-chemistry+sabrash==richmond.edu[*]ccl.net] On Behalf Of Serdar >> Badoglu serdarbadoglu!A!gmail.com >> Sent: Friday, March 15, 2013 1:24 PM >> To: Abrash, Sam >> Subject: CCL:G: DFT and MP2 >> >> >> >> >> >> 6-31G* worked. I have observed that I get error when I add diffuse >> functions on heavy atoms. But I need them. I was aimed to do my calculations >> with 6-311++G** basis set, because that was the set I have used in my DFT >> calculations and I want to see the difference between both methods. I'll try >> to reach that level by increasing the polarity and diffuse functions step by >> step until I reach the limits of my pc. >> >> >> >> Thank you all. >> >> >> >> On Fri, Mar 15, 2013 at 10:31 AM, Stephan Ehrlich >> stephan.ehrlich]_[uni-muenster.de wrote: >> >> >> Sent to CCL by: "Stephan Ehrlich" [stephan.ehrlich],[uni-muenster.de] >> Dear Serdar, >> >> while it apparently solves your technical problem, I would strongly >> discourage >> you from trusting the results of an MP2/3-21g calculation. The basis is >> much >> too small and does not account for correlation properly. >> It also completely lacks polarization functions. Using it will lead to >> large basis set >> superposition and incompleteness errors (BSSE and BSIE). >> I would suggest a basis set of at least triple-zeta quality, with >> polarization >> functions (and augmented with diffuse functions when you are looking at >> non-covalent >> interactions). As an example, the correlation-consistent basis sets by >> Dunning and co-workers >> (e.g. cc-pVTZ and aug-cc-pVTZ in this case) fulfill these criteria. I am >> no Gaussian expert, >> but sure that they are implemented in Gaussian. >> >> Cheers and good luck, >> >> Stephan. >> >> >> >> >> On Fri, 15 Mar 2013 02:53:00 +0100, Serdar Badoğlu serdarbadoglu() >> gmail.com wrote: >> >> I haven't seen such a message. >> >> Finally there's hope for me. I have changed the command line as # opt freq >> mp2/3-21g geom=connectivity, memory settings stayed the same. Finished >> successfully in 20 minutes. >> >> >> >> ____________________________________________________________ >> Stephan Ehrlich (stephan.ehrlich__thch.uni-bonn.de) >> Mulliken Center for Theoretical Chemistry >> Institut fuer Physikalische und Theoretische Chemie >> Universitaet Bonn, Beringstr. 4, D-53115 Bonn, Germany >> ____________________________________________________________
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> >> >> >> >> >> -- >> Serdar BADOĞLU, Ph.D. >> Gazi Üniversitesi Fizik Bölümü > > > > > -- > Serdar BADOĞLU, Ph.D. > Gazi Üniversitesi Fizik Bölümü