From chemistry-request@server.ccl.net Fri Nov 22 15:54:09 2002 Received: from mtiwmhc12.worldnet.att.net ([204.127.131.116]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAMKs9721493 for ; Fri, 22 Nov 2002 15:54:09 -0500 Received: from dopetec ([138.23.156.82]) by mtiwmhc12.worldnet.att.net (InterMail vM.5.01.05.xx 201-253-122-126-xxx-20020920) with ESMTP id <20021122205347.SAQL13933.mtiwmhc12.worldnet.att.net@dopetec> for ; Fri, 22 Nov 2002 20:53:47 +0000 Message-ID: <05bb01c29269$4e512f80$529c178a@dopetec> From: "Donald Keidel" To: Subject: Linux cluster running gaussian 98 Date: Fri, 22 Nov 2002 12:54:09 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_05B8_01C29226.3F6F3360" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_05B8_01C29226.3F6F3360 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all, I am wondering if anyone on the CCL has constructed a Linux cluster of = computers and installed gaussian 98 in a parallel fashion across this = cluster. I went to the Gaussian home page and read the white paper on = parallel execution with Linda and it mentioned that the gaussian = software was written for many platforms and linux based platforms was = not on the list. Is it possible to parallelize gaussian ona linux = cluster and if so can you point me to some good information on the = subject. Thank you to all in advance and have a great day. Don -------------------------------------------------------------------------= -------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_05B8_01C29226.3F6F3360 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello all,

I am wondering if anyone on the CCL has = constructed=20 a Linux cluster of computers and installed gaussian 98 in a parallel = fashion=20 across this cluster. I went to the Gaussian home page and read the = white=20 paper on parallel execution with Linda and it mentioned that the = gaussian=20 software was written for many platforms and linux based platforms was = not on the=20 list. Is it possible to parallelize gaussian ona linux cluster and = if so=20 can you point me to some good information on the subject. Thank = you to all=20 in advance and have a great day.

Don

----------------------------------------------------------------= -----------------------------------------------
Donald=20 J. Keidel
University of California, Riverside
Department of = Biochemistry=20 and Molecular Biology
Riverside, CA 92521
phone: (909)=20 787-5493
fax: (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= /FONT>

------=_NextPart_000_05B8_01C29226.3F6F3360-- From chemistry-request@server.ccl.net Fri Nov 22 18:27:09 2002 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAMNR8724891 for ; Fri, 22 Nov 2002 18:27:09 -0500 Received: from daveg.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id gAMNRI516702; Fri, 22 Nov 2002 15:27:18 -0800 Message-Id: <5.2.0.9.0.20021122150523.03402060@mail.cachesoftware.com> X-Sender: daveg@mail.cachesoftware.com X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Fri, 22 Nov 2002 15:26:06 -0800 To: "Adel El-Azhary" From: David Gallagher Subject: Re: Conformational search, Alchemy 2000 vs MM3 Cc: In-Reply-To: <000c01c2915d$12715b00$8515000a@ksu.edu.sa> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_23946932==.ALT" --=====================_23946932==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Adel, CONFLEX (H. Goto & E. Osawa, J. Chem. Soc. Perkin Trans 2, 187-198, 1993) in BioMedCAChe automatically generates all ring conformations, then energy minimizes them with MM3 or MM2, discards redundant structures and saves a list of all minima (within a specified range) including the global minimum. The process is fully automated and can be performed on a whole batch of molecules with just a single mouse click. The calculations can run on Windows, Macintosh or a UNIX server. An evaluation version of BioMedCAChe is available from http://www.cachesoftware.com/biomedcache/index.shtml David Gallagher, Fujitsu At 03:54 PM 11/21/2002 +0300, Adel El-Azhary wrote: >Deae CCL users: > >I am doing conformational search using the Alchemy 2000 program. It looks >that my molecule has a large ring of 18 atoms and the number of possible >conformations is quite large and taking a quite lot of effort. This is >because I create say 200 conformations and then do MM3 geometry >optimization on each manually and then examine each output. I have to >repeat this step for about a 100 time. I was thinking that the MM3(2000) >program running on unix might be more firiendly. Does anyone has a >suggestion or a similar experience. > >Best regards, > >Adel El-Azhary --=====================_23946932==.ALT Content-Type: text/html; charset="us-ascii" Hi Adel,

CONFLEX (H. Goto & E. Osawa, J. Chem. Soc. Perkin Trans 2, 187-198, 1993) in BioMedCAChe automatically generates all ring conformations, then energy minimizes them with MM3 or MM2, discards redundant structures and saves a list of all minima (within a specified range) including the global minimum. The process is fully automated and can be performed on a whole batch of molecules with just a single mouse click. The calculations can run on Windows, Macintosh or a UNIX server. An evaluation version of BioMedCAChe is available from http://www.cachesoftware.com/biomedcache/index.shtml

David Gallagher, Fujitsu

At 03:54 PM 11/21/2002 +0300, Adel El-Azhary wrote:

Deae CCL users:

I am doing conformational search using the Alchemy 2000 program. It looks that my molecule has a large ring of 18 atoms and the number of possible conformations is quite large and taking a quite lot of effort. This is because I create say 200 conformations and then do MM3 geometry optimization on each manually and then examine each output. I have to repeat this step for about a 100 time. I was thinking that the MM3(2000) program running on unix might be more firiendly. Does anyone has a suggestion or a similar experience.

Best regards,

Adel El-Azhary

--=====================_23946932==.ALT--