From chemistry-request@ccl.net Thu Sep 23 08:20:39 2004 Received: from alkali.kaist.ac.kr (alkali.kaist.ac.kr [143.248.37.171]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8NDKa0a026157 for ; Thu, 23 Sep 2004 08:20:37 -0500 Received: from ilsun (ilsun.kaist.ac.kr [143.248.37.227]) by alkali.kaist.ac.kr (8.12.8/8.12.8) with ESMTP id i8NE6eKq012582 for ; Thu, 23 Sep 2004 23:06:40 +0900 From: "Ilsun Yoon" To: Subject: CCL:about the counterpoise method for BSSE correction Date: Thu, 23 Sep 2004 22:29:53 +0900 Message-ID: <000001c4a171$692deb90$e325f88f@ilsun> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C4A1BC.D9159390" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=1.2 required=7.5 tests=HTML_FONTCOLOR_UNKNOWN, HTML_FONT_FACE_BAD,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C4A1BC.D9159390 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear All, I'm a novice at the Gaussian computation. I hope to calculate the binding energy between water and some organic molecules at the MP2 level of theory. Recently, I tried to use the counterpoise method in G03 for BSSE correction of this calculation. Even though there was no error message in the output log file, I don't know whether my Gaussian input file is right and output data is credible or not. Please let me know the exact way for counterpoise method. Thank you in advance, Ilsun Yoon My Gaussian input for p-cresol and water complex is following (with assumption that this geometry is optimized.) %NProc=2 %Mem=512MB %chk=cresol.chk %rwf=a,2000MB,b,2000MB # RMP2/6-31G** Counterpoise=2 Counterpoise method test for cresol 0 1 C 0 0.038147 2.994492 -1.622849 1 C 0 -0.093231 1.626541 -1.009415 1 C 0 -1.268738 0.882339 -1.160583 1 C 0 0.921021 1.095825 -0.200623 1 C 0 -1.427109 -0.361664 -0.548553 1 C 0 0.779846 -0.142685 0.419312 1 C 0 -0.400757 -0.875610 0.253662 1 O 0 -0.487717 -2.084442 0.884735 1 H 0 0.940536 3.370255 -1.410492 1 H 0 -0.669113 3.596832 -1.251343 1 H 0 -0.069427 2.926987 -2.614624 1 H 0 -2.067307 1.270966 -1.783875 1 H 0 1.843292 1.652130 -0.070251 1 H 0 -2.338394 -0.931015 -0.681366 1 H 0 1.566269 -0.558685 1.036697 1 H 0 0.314682 -2.306198 1.391968 1 O 0 1.874695 -2.683197 2.329926 2 H 0 1.417679 -2.838882 3.162994 2 H 0 2.019485 -3.560532 1.958618 2 Without any error, I had the following in the output file. Counterpoise: corrected energy = -421.934568816558 Counterpoise: BSSE energy = 0.005633789158 ------=_NextPart_000_0001_01C4A1BC.D9159390 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear All,

I’m a novice at the Gaussian computation. I =
hope to calculate the binding

energy=
 between water and some organic =
molecules at the MP2 level of =
theory.

Recently, I tried to use the =
counterpoise method in G03 for BSSE correction of this =
calculation.

Even though there was no error message =
in the output log file, I don’t know whether my Gaussian input =
file is right and output data is credible or =
not.

Please let me know the exact way for =
counterpoise method.

Thank you in = advance,

Ilsun<=
/font> =
Yoon

My Gaussian input for p-cresol and = water complex is following (with assumption that this geometry is = optimized.)

%NProc=3D2

%Mem=3D512MB

%chk=3Dcresol.chk

%rwf=3Da,2000MB,b,2000MB

=
# RMP2/6-31G** =
Counterpoise=3D2

Counterpoise method test for = cresol

0 = 1

C 0    0.038147    2.994492   -1.622849        =
;   1

C 0   -0.093231    1.626541   -1.009415         =
;  1

C 0   -1.268738    0.882339   -1.160583         =
;  1

C 0    0.921021    1.095825   -0.200623         =
;  1

C 0   -1.427109   -0.361664   -0.548553         =
;   1

C 0    0.779846   -0.142685    0.419312         =
;  1

C 0   -0.400757   -0.875610    0.253662         =
;  1

O 0   -0.487717   -2.084442    0.884735         =
;  1

H 0    0.940536    3.370255   -1.410492         =
;  1

H 0   -0.669113    3.596832   -1.251343         =
;  1

H 0   -0.069427    2.926987   -2.614624         =
;  1

H 0   -2.067307    1.270966   -1.783875         =
;  1

H 0    1.843292    1.652130   -0.070251         =
;  1

H 0   -2.338394   -0.931015   -0.681366         =
;   1

H 0    1.566269   -0.558685    1.036697         =
;  1

H 0    0.314682   -2.306198    1.391968         =
;  1

O 0    1.874695   -2.683197    2.329926         =
; 2

H 0    1.417679   -2.838882    3.162994         =
;  2

H 0    2.019485   -3.560532    1.958618         =
;  2

Without any error, I had the following in = the output file.

Counte= rpoise: corrected energy =3D -421.934568816558

Counterpoise:= BSSE energy =3D 0.005633789158

&nbs= p; = ; = &= nbsp; &n= bsp; &nb= sp; &nbs= p; = ;

------=_NextPart_000_0001_01C4A1BC.D9159390-- From chemistry-request@ccl.net Thu Sep 23 15:09:51 2004 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8NK9nEN022257 for ; Thu, 23 Sep 2004 15:09:50 -0500 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id i8NJZR728020 for ; Thu, 23 Sep 2004 13:35:29 -0600 Message-ID: <41532FFA.3000906$at$eyesopen.com> Date: Thu, 23 Sep 2004 14:20:10 -0600 From: George Vacek Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY$at$ccl.net Subject: WABE 1.3 - electrostatics optimization of a lead compound Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net OpenEye Scientific Software, Inc. announces the release of WABE 1.3, a lead optimization program that generates analogs with the same shape but more desirable electrostatics. WABE is useful for exploring the chemical space around a lead compound to elucidate candidates with improved drug profiles or novel scaffolds to avoid patent coverage. "WABE has been shown to be capable of reproducing jumps between known patent classes for several important drugs," says OpenEye's Roger Sayle. WABE quickly generates large numbers of isosteric analogs to a lead molecule, using a graph-invariant replacement algorithm. The method resembles the process of chemical substitution, e.g. carboxylate to amide or amidine, used in medicinal chemistry to create sets of molecules having the same physical shape but varying in electrostatics. WABE then scores the analogs by electrostatic similarity to a known binder or by protein-ligand binding. The similarities between analogs eliminate computationally demanding terms, so WABE efficiently scores over 10,000 analogs per second. WABE can also constrain the atom replacement to certain parts of the lead molecule, which is quite useful when elaborating structure activity relationship (SAR). Sayle points out, "WABE captures all the important SAR for a variety of systems, including methotrexate analogs binding to dihydrofolate reductase and for recently published inhibitors to Lck kinase." For further information, please visit www.eyesopen.com or contact business$at$eyesopen.com. Regards, George Vacek VP, Business Development OpenEye Scientific Software From chemistry-request@ccl.net Thu Sep 23 07:07:52 2004 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8NC7o0a020993 for ; Thu, 23 Sep 2004 07:07:51 -0500 Received: by leitl.org (Postfix, from userid 500) id D9A353A84E3; Thu, 23 Sep 2004 14:18:20 +0200 (CEST) Date: Thu, 23 Sep 2004 14:18:19 +0200 From: Eugen Leitl To: chemistry=at=ccl.net Subject: Re: [Beowulf] Beowulf Application in the Sciences (fwd from rgb=at=phy.duke.edu) Message-ID: <20040923121818.GU1457=at=leitl.org> ----- Forwarded message from "Robert G. Brown" ----- From: "Robert G. Brown" Date: Thu, 23 Sep 2004 08:04:17 -0400 (EDT) To: Timo Mechler Cc: beowulf=at=beowulf.org Subject: Re: [Beowulf] Beowulf Application in the Sciences On Wed, 22 Sep 2004, Timo Mechler wrote: > Hello all, > > Through my studies of computer clusters so far, it has become apparent to > me that a lot of applications exist in both the Math and Physics fields > (e.g. different types modeling, for instance in high energy physics, > etc.). I'm now really wondering what kind of applications exist in the > other physical sciences such as biology and chemistry. How would clusters > be benefical in these areas? I would greatly appreciate if someone could > provide me with a few examples and some insight. Curiously enough, Cluster World Magazine devoted an issue quite recently to computational chemistry. Cluster computing is alive and well there, especially in areas that overlap in various ways with physics, e.g. quantum chemistry and molecular dynamics, as well as structural modelling and more. Biology, too, has many clusters serving many purposes. There are "biogrid" projects that range from departmental to national in scope; see e.g. http://www.ncbiogrid.org/ for North Carolina's biogrid project home page. These projects typically focus on e.g. genomics and bioinformatics, but there are also clusters that I'm aware of at Duke that study e.g. conduction patterns in heart tissue (solving the poisson equation in inhomogeneous media in a distributed way), biomolecular folding, and a lot of other things in smaller projects more like what one would typically find in math or physics or chemistry. If you google a bit, see if you can scare up a copy of the relevant CWM, and ask around at area universities or ask the contacts at things like biogrid or chemstry grid projects, you can doubtless refine you knowledge of this as much as you like. Clusters and their larger multidisciplinary variants the grids are firmly established in pretty much all the hard sciences and engineering these days, to the point where many campuses (like Duke) are experiencing explosive growth in the number and type of clusters. Duke has its own internal grid project and a center that has recently been set up to coordinate and house and permit sharing of clusters purchased by individual groups across the sciences, engineering and medicine (see www.csem.duke.edu). This center can barely keep up with the growth as groups all over campus are getting twenty nodes here, a hundred nodes there. It coordinates cluster management and facilitates computational science work done on grids and ways of managing distributed resources -- most of its toplevel staff have graduate experience and/or degrees in a variety of sciences and have some decades of cluser experience between them. Many of them are frequent contributors to and familiar names on this list. This is actually a very exciting time for cluster computing -- it is undergoing something of a paradigm shift from the "beowulf" model that has somewhat dominated the last eight years back into a model that is both older (distributed parallel computing and compute farms of various sorts predated beowulf per se by many years) and newer (they never had to cope with authentication, security, batch job coordination over a wide range of projects with a wide range of resource constraints being run on a heterogeneous collection of resources contributed AND OWNED by many individuals with their own agendas and usage priorities;-). It is amusing to contemplate where this is going. In ten years will there just be "the Grid" as there is now the Internet, where we install a toplevel application to join our computer(s) to the grid and transparently offer up idle cycles to others in exchange for transparently picking up their idle cycles in return (all nice and secure and sandboxed)? Will we start to see a Gibsonesque turn, where rogue/viral programs released into this grid become a strange form of virtual "life"? Stay tuned to this channel... (Damn, I need to just put these replies straight into my CWM column. Kill two birds with one stone, so to speak;-). > > My other question is in regards to parallel programming. Are there some > free parallel programs out there that one can download to run on a > cluster, or are most of the programs run on clusters "homegrown"? There are plenty of free parallel programs you can run for fun or specific purposes, some commercial parallel programs ditto, and yes, there are lots of homegrown ones. PVM and MPI sites will typically come with some of the former or contain links to them, big projects (like biogrid stuff) attract some commercial effort although there are also frequently GPL tools available as well. Homebrew abounds mostly because a topically focussed physics computation (for example) is almost always a one-off -- you code your particular bit of science in competition with everybody else. There are exceptions to this, of course, where groups use the same basic tool to look at different things, but it's pretty common to write or port your own code. rgb > > Thanks in advance for your help. > > -Timo Mechler > > -- > Timo R. Mechler > mechti01=at=luther.edu > > > _______________________________________________ > Beowulf mailing list, Beowulf=at=beowulf.org > To change your subscription (digest mode or unsubscribe) visit http://www= .beowulf.org/mailman/listinfo/beowulf > Robert G. Brown http://www.phy.duke.edu/~rgb/ Duke University Dept. of Physics, Box 90305 Durham, N.C. 27708-0305 Phone: 1-919-660-2567 Fax: 919-660-2525 email:rgb=at=phy.duke.edu _______________________________________________ Beowulf mailing list, Beowulf=at=beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.b= eowulf.org/mailman/listinfo/beowulf ----- End forwarded message ----- -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net