From owner-chemistry@ccl.net Wed Jul 28 01:02:00 2010 From: "Tapas Kar tapas.kar(0)usu.edu" To: CCL Subject: CCL:G: Computational cost for CCSD(T) Message-Id: <-42366-100728010005-19462-UI6tqm9BNCzcdESD3ZqyzQ^server.ccl.net> X-Original-From: Tapas Kar Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_929483FB2C66F741972CF3CE351D3C443B83211EDDexchgbe03aggi_" Date: Tue, 27 Jul 2010 23:00:00 -0600 MIME-Version: 1.0 Sent to CCL by: Tapas Kar [tapas.kar_._usu.edu] --_000_929483FB2C66F741972CF3CE351D3C443B83211EDDexchgbe03aggi_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Thanks Jamin, I forgot to mention that I am dealing with radicals (open-shell cases). ________________________________ > From: owner-chemistry+tapas.kar=3D=3Dusu.edu(_)ccl.net [mailto:owner-chemistr= y+tapas.kar=3D=3Dusu.edu(_)ccl.net] On Behalf Of Jamin Krinsky jamink^^berkel= ey.edu Sent: Tuesday, July 27, 2010 5:18 PM To: Tapas Kar Subject: CCL:G: Computational cost for CCSD(T) Hi Tapas, To give you an idea, on our system a 24-atom molecule with 250 basis functi= ons (about 530 primitives), run on 6 AMD Istanbul cores with 23GB RAM (all = this is shared, not network), took about 50 cpu hours (total) and generated= a 60GB rwf file. Now consider that CCSD(T) has an ON^3 disk requirement... Maybe this helps somewhat. Jamin On Tue, Jul 27, 2010 at 3:31 PM, Tapas Kar tapas.kar!A!usu.edu > wrote= : Sent to CCL by: "Tapas Kar" [tapas.kar(~)usu.edu] Hello experts, Any idea on how many cpu hours may require for CCSD(T) calculation on molec= ules with 330 to 410 basis functions (about 500-600 primitive Gaussian) usi= ng 16/24/32 processors in G09. Any suggestion on memory, scratch disk space= and processors may require for such calculations? Thanks Tapas -=3D This is automatically added to each message by the mailing script =3D-=
= or use:E-mail to administrators: CHEMISTRY-REQUEST]|[ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml, 510-643-0616 http://glab.cchem.berkeley.edu --_000_929483FB2C66F741972CF3CE351D3C443B83211EDDexchgbe03aggi_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Thanks Jamin,=

I forgot to mention that I am dealing = with radicals (open-shell cases).

 

From: owner-chemistry+tapas.kar=3D=3Dusu.edu(_)ccl.net [mailto:owner-chemistry+tapas.kar=3D=3Dusu.edu(_)ccl.net] On Behalf Of Jamin Krinsky jamink^^berkeley.edu
Sent: Tuesday, July 27, 2010= 5:18 PM
To: Tapas Kar
Subject: CCL:G: Computationa= l cost for CCSD(T)

 

Hi Tapas,

To give you an idea, on our system a 24-atom molecule with 250 basis functi= ons (about 530 primitives), run on 6 AMD Istanbul cores with 23GB RAM (all this= is shared, not network), took about 50 cpu hours (total) and generated a 60GB = rwf file. Now consider that CCSD(T) has an ON^3 disk requirement...

Maybe this helps somewhat.

Jamin

On Tue, Jul 27, 2010 at 3:31 PM, Tapas Kar tapas.kar!A!usu.edu <owner-chemistry]|[ccl.net> wrote:


Sent to CCL by: "Tapas  Kar" [tapas.kar(~)usu.edu]
Hello experts,
Any idea on how many cpu hours may require for CCSD(T) calculation on molec= ules with 330 to 410 basis functions (about 500-600 primitive Gaussian) using 16/24/32 processors in G09. Any suggestion on memory, scratch disk space an= d processors may require for such calculations?

Thanks
Tapas



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


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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

--_000_929483FB2C66F741972CF3CE351D3C443B83211EDDexchgbe03aggi_-- From owner-chemistry@ccl.net Wed Jul 28 04:03:00 2010 From: "Thomas Gkourmpis thomas.gkourmpis{}borealisgroup.com" To: CCL Subject: CCL:G: NewZmat Conversion Problem Message-Id: <-42367-100728040146-3055-GyuDu+/fWHKSE7wpl7drag=-=server.ccl.net> X-Original-From: "Thomas Gkourmpis" Date: Wed, 28 Jul 2010 04:01:43 -0400 Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis~!~borealisgroup.com] Hello everyone I seem to have a problem in using the NewZmat Conversion routine in Gaussian03W, and I really don't understand what I am doing wrong (something obviously, but I can't really get it). I am trying to convert a checkpoint file to gjf and pdb files for usage in the ChemRate program to calculate the reaction rate parameters of a particular reaction. I go to the Utilities Tab in Gaussian, chose NewZmat and I am just pressing the convert button to convert the file in question to the format I need (chosen from the Options Menu). There I get a message on the Gaussian window that the processing is complete but nothing actually happens. No converted file can be found on the appropriate directory (in any directory actually I did search them all) and no error message. I am at loss here. Any ideas or suggestions on what I am doing wrong? (this is the first time I am using NewZmat) Thanks in advance Thomas From owner-chemistry@ccl.net Wed Jul 28 05:42:05 2010 From: "Andreas Klamt klamt[a]cosmologic.de" To: CCL Subject: CCL:G: Computational cost for CCSD(T) Message-Id: <-42368-100728053410-13733-38Pe7fmOgiRS0g/8Q3xFcw[-]server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=ISO-8859-15 Date: Wed, 28 Jul 2010 11:34:02 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt(0)cosmologic.de] Hi Tapas,


the numbers reported by Jamin with respect to CCSD(T) in Gaussian seem rather high to us.  We do not have Gaussain09 here, but just for comparison, with the efficient recent implementation of CCSD(T) in TURBOMOLE6.2 we have done a single point (Jamin does not report whether his numbers are for single point, as we assume, or for geometry optimization) for a system with 18 atoms and 480 basis functions (CAOs) in 44 hours on a single processor Intel Xeon[*]2.50GHz using less than 1.7GB RAM. We are not sure about the disk space used, but this was not crucial. Please note that our system had almost twice as many basis functions as Jamin reported!


Andreas


Am 28.07.2010 07:00, schrieb Tapas Kar tapas.kar(0)usu.edu:

Thanks Jamin,

I forgot to mention that I am dealing with radicals (open-shell cases).

 

From: owner-chemistry+tapas.kar==usu.edu\a/ccl.net [mailto:owner-chemistry+tapas.kar==usu.edu\a/ccl.net] On Behalf Of Jamin Krinsky jamink^^berkeley.edu
Sent: Tuesday, July 27, 2010 5:18 PM
To: Tapas Kar
Subject: CCL:G: Computational cost for CCSD(T)

 

Hi Tapas,

To give you an idea, on our system a 24-atom molecule with 250 basis functions (about 530 primitives), run on 6 AMD Istanbul cores with 23GB RAM (all this is shared, not network), took about 50 cpu hours (total) and generated a 60GB rwf file. Now consider that CCSD(T) has an ON^3 disk requirement...

Maybe this helps somewhat.

Jamin

On Tue, Jul 27, 2010 at 3:31 PM, Tapas Kar tapas.kar!A!usu.edu <owner-chemistry]|[ccl.net> wrote:


Sent to CCL by: "Tapas  Kar" [tapas.kar(~)usu.edu]
Hello experts,
Any idea on how many cpu hours may require for CCSD(T) calculation on molecules with 330 to 410 basis functions (about 500-600 primitive Gaussian) using 16/24/32 processors in G09. Any suggestion on memory, scratch disk space and processors may require for such calculations?

Thanks
Tapas




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--
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



-- 
PD. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt[*]cosmologic.de
web    	www.cosmologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
From owner-chemistry@ccl.net Wed Jul 28 12:32:01 2010 From: "Jamin Krinsky jamink*_*berkeley.edu" To: CCL Subject: CCL:G: Computational cost for CCSD(T) Message-Id: <-42369-100728123019-28387-FAuvLxUTZjyho1/Dvhd6yA-.-server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=001636e0b4b5c1c106048c75219f Date: Wed, 28 Jul 2010 09:30:11 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink]^[berkeley.edu] --001636e0b4b5c1c106048c75219f Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Tapas, Andreas, Sorry, the numbers are for a SP calculation, as analytical gradients are no= t available for the triples in CCSD(T). 44 hours total running serial vs 50 hours total running parallel is not too bad, if the system sizes were the same at least. Also I'm pretty sure that a single-processor Xeon is much faster than each AMD (Istanbul) core on a 6-core chip. As far as I know these calculations in G09 are not actually very RAM intensive, that is just the allocation we can use for 6 processors so that'= s what I happened to use in that case. I have heard from various people that Gaussian's CCSD implementation is not very efficient, but I don't normally use the method in my own research so I'm not inclined (or prepared) to give any opinion on that, and I'm certainly not going to publish such an opinion on-line. It might be true or it might just be Gaussian-hating. Jamin On Wed, Jul 28, 2010 at 2:34 AM, Andreas Klamt klamt[a]cosmologic.de < owner-chemistry,ccl.net> wrote: > Sent to CCL by: Andreas Klamt [klamt(0)cosmologic.de] > Hi Tapas, > > > the numbers reported by Jamin with respect to CCSD(T) in Gaussian seem > rather high to us. We do not have Gaussain09 here, but just for comparis= on, > with the efficient recent implementation of CCSD(T) in TURBOMOLE6.2 we ha= ve > done a single point (Jamin does not report whether his numbers are for > single point, as we assume, or for geometry optimization) for a system wi= th > 18 atoms and 480 basis functions (CAOs) in 44 hours on a single processor > Intel Xeon:2.50GHz using less than 1.7GB RAM. We are not sure about the > disk space used, but this was not crucial. Please note that our system ha= d > almost twice as many basis functions as Jamin reported! > > > Andreas > > > Am 28.07.2010 07:00, schrieb Tapas Kar tapas.kar(0)usu.edu: > > Thanks Jamin, > > I forgot to mention that I am dealing with radicals (open-shell cases). > > > ------------------------------ > > *From:* owner-chemistry+tapas.kar=3D=3Dusu.edu\a/ccl.net [ > mailto:owner-chemistry+tapas.kar=3D=3Dusu.edu\a/ccl.net] > *On Behalf Of *Jamin Krinsky jamink^^berkeley.edu > *Sent:* Tuesday, July 27, 2010 5:18 PM > *To:* Tapas Kar > *Subject:* CCL:G: Computational cost for CCSD(T) > > > > Hi Tapas, > > To give you an idea, on our system a 24-atom molecule with 250 basis > functions (about 530 primitives), run on 6 AMD Istanbul cores with 23GB R= AM > (all this is shared, not network), took about 50 cpu hours (total) and > generated a 60GB rwf file. Now consider that CCSD(T) has an ON^3 disk > requirement... > > Maybe this helps somewhat. > > Jamin > > On Tue, Jul 27, 2010 at 3:31 PM, Tapas Kar tapas.kar!A!usu.edu < > owner-chemistry]|[ccl.net > wrote: > > > Sent to CCL by: "Tapas Kar" [tapas.kar(~)usu.edu] > Hello experts, > Any idea on how many cpu hours may require for CCSD(T) calculation on > molecules with 330 to 410 basis functions (about 500-600 primitive Gaussi= an) > using 16/24/32 processors in G09. Any suggestion on memory, scratch disk > space and processors may require for such calculations? > > Thanks > Tapas > > > > > E-mail to subscribers: CHEMISTRY]|[ccl.net or > use:> > E-mail to administrators: CHEMISTRY-REQUEST]|[ccl.netor use>
> > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink]|[berkeley.edu , 510-643-0616 > http://glab.cchem.berkeley.edu > > > > -- > PD. Dr. Andreas Klamt > CEO / Gesch=E4ftsf=FChrer > COSMOlogic GmbH & Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt:cosmologic.de > web www.cosmologic.de > > HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt > > -=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 the > strange characters on the top line to the , sign. You can also look up th= e > X-Original-From: line in the mail header. E-mail to subscribers: > CHEMISTRY,ccl.net or use:= E-mail to administrators: > CHEMISTRY-REQUEST,ccl.net or useBefore posting, check wait > time at: http://www.ccl.netConferences: > http://server.ccl.net/chemistry/announcements/conferences/ Search > Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your mail > bounces from CCL with 5.7.1 error, check:= RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ --=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 --001636e0b4b5c1c106048c75219f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Tapas, Andreas,

Sorry, the numbers are for a SP calculation, as anal= ytical gradients are not available for the triples in CCSD(T). 44 hours tot= al running serial vs 50 hours total running parallel is not too bad, if the= system sizes were the same at least. Also I'm pretty sure that a singl= e-processor Xeon is much faster than each AMD (Istanbul) core on a 6-core c= hip.

As far as I know these calculations in G09 are not actually very RAM in= tensive, that is just the allocation we can use for 6 processors so that= 9;s what I happened to use in that case.

I have heard from various = people that Gaussian's CCSD implementation is not very efficient, but I= don't normally use the method in my own research so I'm not inclin= ed (or prepared) to give any opinion on that, and I'm certainly not goi= ng to publish such an opinion on-line. It might be true or it might just be= Gaussian-hating.

Jamin


On Wed, Jul 28, 2010 at 2:3= 4 AM, Andreas Klamt klamt[a]cosmologic.de<= /a> <owner-= chemistry,ccl.net> wrote:
Sent to CCL by: Andreas Klamt [klamt(0)cosmologic.de] =20
Hi Tapas,


the numbers reported by Jamin with respect to CCSD(T) in Gaussian seem rather high to us.=A0 We do not have Gaussain09 here, but just for comparison, with the efficient recent implementation of CCSD(T) in TURBOMOLE6.2 we have done a single point (Jamin does not report whether his numbers are for single point, as we assume, or for geometry optimization) for a system with 18 atoms and 480 basis functions (CAOs) in 44 hours on a single processor Intel Xeon:2.50= GHz using less than 1.7GB RAM. We are not sure about the disk space used, but this was not crucial. Please note that our system had almost twice as many basis functions as Jamin reported!


Andreas


Am 28.07.2010 07:00, schrieb Tapas Kar tapas.kar(0)usu.edu:
=20 =20 =20 =20 =20 =20

Thanks Jamin= ,

I forgot to mention that I am dealing with radicals (open-shell cases).

=A0

<= font face=3D"Times New Roman" size=3D"3">

From: owner-chemistry+tapas.kar=3D=3Dusu.edu\a/ccl.net [mailto:owner-chemistry+tapas.kar=3D=3Dusu.edu\a/ccl.net] = On Behalf Of Jamin Krinsky jamink^^berkeley.edu<= br> Sent: Tuesday, July 27, 2010 5:18 PM
To: Tapas Kar
Subject: CCL:G: Computational cost for CCSD(T)

=A0

Hi Tapas,

To give you an idea, on our system a 24-atom molecule with 250 basis functions (about 530 primitives), run on 6 AMD Istanbul cores with 23GB RAM (all this is shared, not network), took about 50 cpu hours (total) and generated a 60GB rwf file. Now consider that CCSD(T) has an ON^3 disk requirement...

Maybe this helps somewhat.

Jamin

On Tue, Jul 27, 2010 at 3:31 PM, Tapas Kar tapas.kar!A!usu.edu <ow= ner-chemistry]|[ccl.net> wrote:


Sent to CCL by: "Tapas =A0Kar" [tapas.kar(~)usu.edu]
Hello experts,
Any idea on how many cpu hours may require for CCSD(T) calculation on molecules with 330 to 410 basis functions (about 500-600 primitive Gaussian) using 16/24/32 processors in G09. Any suggestion on memory, scratch disk space and processors may require for such calculations?

Thanks
Tapas


=20

E-mail to subscribers: CHEMISTRY]|[ccl.net or use:
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--
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink]|= [berkeley.edu, 510-643-0616
http://glab.= cchem.berkeley.edu



--=20
PD. Dr. Andreas Klamt
CEO / Gesch=E4ftsf=FChrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt:cosm=
ologic.de
web    	www.cosmolog=
ic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
-=3D This is automatically added to each message by the mailing script =3D-E-mail to subscribers: CHEMISTRY,ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST,ccl.net or use http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.n= et/jobs=20 Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://= 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

--001636e0b4b5c1c106048c75219f-- From owner-chemistry@ccl.net Wed Jul 28 13:07:00 2010 From: "Pablo A. Denis pablod(-)fq.edu.uy" To: CCL Subject: CCL: Computational cost for CCSD(T) Message-Id: <-42370-100728083537-2225-E/2kdxRdWHyZwKi/UaeVRg-#-server.ccl.net> X-Original-From: "Pablo A. Denis" Date: Wed, 28 Jul 2010 09:35:18 -0300 Sent to CCL by: "Pablo A. Denis" [pablod#,#fq.edu.uy] Hi Tapas, are these molecules symmetric? that can reduce the computation time drastically... Also, the number of e- is important best regards, pablo From owner-chemistry@ccl.net Wed Jul 28 13:41:01 2010 From: "Gerald Knizia knizia###theochem.uni-stuttgart.de" To: CCL Subject: CCL:G: Computational cost for CCSD(T) Message-Id: <-42371-100728131810-319-3vaqPnbq5WNCZfQkWGszWA[]server.ccl.net> X-Original-From: Gerald Knizia Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 28 Jul 2010 19:17:56 +0200 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia~!~theochem.uni-stuttgart.de] On Wednesday 28 July 2010 00:31, Tapas Kar tapas.kar!A!usu.edu wrote: > Sent to CCL by: "Tapas Kar" [tapas.kar(~)usu.edu] > Hello experts, > Any idea on how many cpu hours may require for CCSD(T) calculation on > molecules with 330 to 410 basis functions (about 500-600 primitive > Gaussian) using 16/24/32 processors in G09. This depends a lot on the molecule (number of occupied orbitals, symmetries, etc). But it can't really be that long. In PCCP 10 3400 (2008) Marchetti and Werner note that their explicitly correlated CCSD(T)-F12 calculation of the benzene dimer with the AVTZ basis set (828 basis functions) took 118h on a single MacPro, using Molpro. -- Gerald Knizia From owner-chemistry@ccl.net Wed Jul 28 14:27:01 2010 From: "Tapas Kar tapas.kar]![usu.edu" To: CCL Subject: CCL: Computational cost for CCSD(T) Message-Id: <-42372-100728142535-1739-/BbYVZ2itiTxflwiCnq7wA+/-server.ccl.net> X-Original-From: Tapas Kar Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 28 Jul 2010 12:25:26 -0600 MIME-Version: 1.0 Sent to CCL by: Tapas Kar [tapas.kar,,usu.edu] Hi Pablo, No they are not symmetric and contain 95 electrons (an open-shell case). Thanks Tapas -----Original Message----- > From: owner-chemistry+tapas.kar==usu.edu-x-ccl.net [mailto:owner-chemistry+tapas.kar==usu.edu-x-ccl.net] On Behalf Of Pablo A. Denis pablod(-)fq.edu.uy Sent: Wednesday, July 28, 2010 6:35 AM To: Tapas Kar Subject: CCL: Computational cost for CCSD(T) Sent to CCL by: "Pablo A. Denis" [pablod#,#fq.edu.uy] Hi Tapas, are these molecules symmetric? that can reduce the computation time drastically... Also, the number of e- is important best regards, pablohttp://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 Wed Jul 28 18:05:01 2010 From: "EMRYS W THOMAS ewt:_:emrys.fslife.co.uk" To: CCL Subject: CCL:G: NewZmat Conversion Problem Message-Id: <-42373-100728145218-30237-fekAZwaXftnFw1X2fksoHQ^-^server.ccl.net> X-Original-From: "EMRYS W THOMAS" Date: Wed, 28 Jul 2010 14:52:15 -0400 Sent to CCL by: "EMRYS W THOMAS" [ewt=-=emrys.fslife.co.uk] Hi Thomas In the first G03W(A01) release the newzmat option often failed-this was fixed in subsequent releases of the program.You must also set your input and output options appropriately before conversion_I assume your'e doing this. Best ET > "Thomas Gkourmpis thomas.gkourmpis{}borealisgroup.com" wrote: > > Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis~!~borealisgroup.com] > Hello everyone > > I seem to have a problem in using the NewZmat Conversion routine in Gaussian03W, and I really don't understand what I am doing wrong (something obviously, but I can't really get it). > > I am trying to convert a checkpoint file to gjf and pdb files for usage in the ChemRate program to calculate the reaction rate parameters of a particular reaction. > > I go to the Utilities Tab in Gaussian, chose NewZmat and I am just pressing the convert button to convert the file in question to the format I need (chosen from the Options Menu). There I get a message on the Gaussian window that the processing is complete but nothing actually happens. No converted file can be found on the appropriate directory (in any directory actually I did search them all) and no error message. > > I am at loss here. Any ideas or suggestions on what I am doing wrong? (this is the first time I am using NewZmat) > > Thanks in advance > > Thomas > > From owner-chemistry@ccl.net Wed Jul 28 22:14:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim(0)compchem.net" To: CCL Subject: CCL:G: NewZmat Conversion Problem Message-Id: <-42374-100728211951-19266-u4+fHzOCz0Y1+GXNA4dF2A=-=server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016363ba7806f5f6a048c7c8767 Date: Thu, 29 Jul 2010 02:19:42 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim()compchem.net] --0016363ba7806f5f6a048c7c8767 Content-Type: text/plain; charset=ISO-8859-1 Dear Thomas I don't use windows version, but I have tested the NewZmat option, and it works well. As I told you I am not expert with Windows version, but I have some idea: * have you tried to use NewZmat utility in linux version. * you can generate the optimized structures from your output and there are a lot of programs can be used to extract the structures from the output (like; Chemcraft), and then you can use OpenBabel to convert the file to the desired file format. * GaussView reads the final optimized structure from the checkpoint file. May be I am missing something here, and hope somebody else able to help you. sincerely; M. Ibrahim On Wed, Jul 28, 2010 at 9:01 AM, Thomas Gkourmpis thomas.gkourmpis{} borealisgroup.com wrote: > > Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis~!~borealisgroup.com] > Hello everyone > > I seem to have a problem in using the NewZmat Conversion routine in > Gaussian03W, and I really don't understand what I am doing wrong (something > obviously, but I can't really get it). > > I am trying to convert a checkpoint file to gjf and pdb files for usage in > the ChemRate program to calculate the reaction rate parameters of a > particular reaction. > > I go to the Utilities Tab in Gaussian, chose NewZmat and I am just pressing > the convert button to convert the file in question to the format I need > (chosen from the Options Menu). There I get a message on the Gaussian window > that the processing is complete but nothing actually happens. No converted > file can be found on the appropriate directory (in any directory actually I > did search them all) and no error message. > > I am at loss here. Any ideas or suggestions on what I am doing wrong? (this > is the first time I am using NewZmat) > > Thanks in advance > > Thomas> > > -- 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 --0016363ba7806f5f6a048c7c8767 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Thomas
I don't use windows version, but I have tested the NewZ= mat option, and it works well.
As I told you I am not expert with= Windows version, but I have some idea:
* have you tried to use N= ewZmat utility in linux version.
* =A0you can generate the optimized structures from your output and th= ere are a lot of programs can be used to extract the structures from the ou= tput (like; Chemcraft), and then you can use OpenBabel to convert the file = to the desired file format.
* GaussView reads the final optimized structure from the checkpoint fi= le.=A0
May be I am missing something here, and hope somebody else= able to help you.
sincerely;
M. Ibrahim



On Wed, Jul 28, 20= 10 at 9:01 AM, Thomas Gkourmpis thomas.gkourmpis{}borealisgroup.com <owner-chemistry,,ccl.net> wrote:

Sent to CCL by: "Thomas =A0Gkourmpis" [thomas.gkourmpis~!~borealisgroup.com]
Hello everyone

I seem to have a problem in using the NewZmat Conversion routine in Gaussia= n03W, and I really don't understand what I am doing wrong (something ob= viously, but I can't really get it).

I am trying to convert a checkpoint file to gjf and pdb files for usage in = the ChemRate program to calculate the reaction rate parameters of a particu= lar reaction.

I go to the Utilities Tab in Gaussian, chose NewZmat and I am just pressing= the convert button to convert the file in question to the format I need (c= hosen from the Options Menu). There I get a message on the Gaussian window = that the processing is complete but nothing actually happens. No converted = file can be found on the appropriate directory (in any directory actually I= did search them all) and no error message.

I am at loss here. Any ideas or suggestions on what I am doing wrong? (this= is the first time I am using NewZmat)

Thanks in advance

Thomas



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=A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 Mahmoud A. A. Ibrahim=A0 =A0 =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=A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 The Un= iversity of Manchester,
=A0 =A0 =A0 =A0=A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 Fa= culty of Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia = University,
=A0 =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 =A0 Egypt.

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=A0 =A0 = =A0 =A0 =A0=A0 Email: m.ibrahim,,c= ompchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 Website: ww= w.compchem.net
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