From owner-chemistry@ccl.net Fri Jun 3 02:44:00 2011 From: "Valentin Alba Aparicio valentin.alba__pas.uned.es" To: CCL Subject: CCL: thermodynamic parameters! Message-Id: <-44827-110603023632-25963-HUq3QXMh9NW7QOz4W67wCQ ~ server.ccl.net> X-Original-From: Valentin Alba Aparicio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 03 Jun 2011 08:36:25 +0200 MIME-Version: 1.0 Sent to CCL by: Valentin Alba Aparicio [valentin.alba|,|pas.uned.es] You'll find a nice explanation here: http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/energy1.htm > Sent to CCL by: "lukman olasunkanmi" [waleolasunkanmi%%gmail.com] > Hello, > Please, can anyone explain why the heat of formation and change in free energy of formation of some simple known compounds like ethene, ethyne, benzene(l,g), HCN, N2O etc are positive and yet they are stable.> > > From owner-chemistry@ccl.net Fri Jun 3 03:48:01 2011 From: "psavita##crlindia.com" To: CCL Subject: CCL: thermodynamic parameters! Message-Id: <-44828-110603024226-28206-ZEtApOORuJwEnBkHTw+nog]-[server.ccl.net> X-Original-From: psavita()crlindia.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Fri, 3 Jun 2011 12:17:47 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita(_)crlindia.com
Hello Lukman,

A simple explanation arises from the fact = that although products you mentioned are at higher energy than the reactant= s,
the barriers to reach them are also high so that the back reaction n= eeds to be activated as well.
In fact, there are multiple stages in a ty= pical reaction, some of which have to be catalytically driven.
The actua= l figures for such barriers can be looked up in the literature.

Than= ks and best wishes,

Savita Pundlik
Computational Materials Applied Research Group
= Computational Research Laboratories Ltd.,
Taco House, Damle Path, Off Law College Road
Pune - 411004, India.

=


-----owner-chemistr= y+psavita=3D=3Dcrlindia.com]*[ccl.net wrote: -----

To: "Pundlik, Savita Sunil -id#3= zd-" <psavita]*[crlindia.com>
From: "lukman olasunkanmi waleolasunk= anmi%x%gmail.com" <owner-chemistry]*[ccl.net>
Sent by: owner-chemistry+psavita=3D=3Dcrlindia.com]*[ccl.net<= br>Date: 06/02/2011 11:15PM
Subject: CCL: thermodynamic parameters!
<= br>
Sent to CCL = by: "lukman  olasunkanmi" [waleolasunkanmi%%gmail.com]
Hello,
Pl= ease, can anyone explain why the heat of formation and change in free energ= y of formation of some simple known compounds like ethene, ethyne, benzene(= l,g), HCN, N2O etc are positive and yet they are stable.



-= =3D This is automatically added to each message by the mailing script =3D-<= br= l= ook up the X-Original-From: line in the mail header.

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= From owner-chemistry@ccl.net Fri Jun 3 08:01:01 2011 From: "Sathvik Harsha sathvik.harsha],[gmail.com" To: CCL Subject: CCL: Help with the choice of Descriptors for clustering Fragments Message-Id: <-44829-110603043737-353-hEB99NJTILi2NMW/jy0j9Q\a/server.ccl.net> X-Original-From: "Sathvik Harsha" Date: Fri, 3 Jun 2011 04:37:34 -0400 Sent to CCL by: "Sathvik Harsha" [sathvik.harsha:-:gmail.com] Dear All, While I know there is no single "exact" good clustering method, I am trying to cluster my molecules (fragments which may be either Ring or ringAssemblies) using Pipeline pilot. Pipeline pilot has has following properties like ECFP_2 ECFP_4 ECFP_6 FCFP_2 FCFP_4 FCFP_6 ALogP Molecular_Weight Num_H_Donors Num_H_Acceptors Num_RotatableBonds MDLPublicKeys Num_Atoms Num_Rings Num_AromaticRings Num_Fragments Molecular_PolarSurfaceArea Molecular_PolarSASA NPlusO_Count I chose Molecular_Weight Num_H_Donors Num_H_Acceptors Num_RotatableBonds NPlusO_Count as my Molecular Properties since my Data set is list of Fragments (Canonical_Smiles) having associated to their parent molecules and the biological assay but I am worried with the Choice of Fingerprint properties. (along with the Molecular properties) I would be glad if someone has suggestions here considering the fact that these are ring Assemblies and rings fragmented from Chemical Databases. having association with the parent molecules (one fragment might have association with many molecules) Thanks for your guidance --Sathvik From owner-chemistry@ccl.net Fri Jun 3 08:36:00 2011 From: "Jun Zhang coolrainbow]*[yahoo.cn" To: CCL Subject: CCL:G: How to build a linux cluster for computational chemistry purposes?, HELP Message-Id: <-44830-110602223114-10798-XstHcwdN24DNtskT8AFyAw-,-server.ccl.net> X-Original-From: Jun Zhang Content-Type: multipart/alternative; boundary="0-325409062-1307068262=:54953" Date: Fri, 3 Jun 2011 10:31:02 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow-$-yahoo.cn] --0-325409062-1307068262=:54953 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Miguel Quiliano: =A0 =A0=A0=A0=A0 I had ever written a very detailed document=A0on cluster build= ing, but it was written in Chinese rather than=A0in English so I don't know= whether it can help you... If you need it, I can send you by e-mail. =A0 Good Luck! Jun Zhang Nankai University coolrainbow[]yahoo.cn Dear community. After... talk.. and talk.. with my boss, I convinced him to build a linux c= luster for computational chemistry purposes, in other words... to use Gauss= ian03. So now I have 80 cores at my disposal. We also have TCP/LINDA. Could you please recommend me, one operative system and some online guide t= o build it or book? Personal experiences are welcome. Thanks in advance. Miguel Quiliano. --0-325409062-1307068262=:54953 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Miguel Quiliano:
 
     I had ever written a very detailed document&n= bsp;on cluster building, but it was written in Chinese rather than in = English so I don't know whether it can help you... If you need it, I can se= nd you by e-mail.
 
Good Luck!

Jun Zhang
Nankai University
coolrainbow[]yahoo.= cn


Dear community.

After... talk.. and talk.. wi= th my boss, I convinced him to build a linux cluster = for computational chemistry purposes, in other words... to use Gaussian03. = So now = I have 80 cores at my disposal. We also have TCP/LINDA.

Could you pl= ease recommend me, one operative system and some online guide to build it o= r book? Personal experiences are welcome.

Thanks in advance.

= Miguel Quiliano.
--0-325409062-1307068262=:54953-- From owner-chemistry@ccl.net Fri Jun 3 09:11:00 2011 From: "=?EUC-KR?B?vK3H9sDP?= fanmusic1(!)gmail.com" To: CCL Subject: CCL:G: calculation Message-Id: <-44831-110603011129-26966-Yj/4JaOTjrh6TH4OxNcDvA.:.server.ccl.net> X-Original-From: =?EUC-KR?B?vK3H9sDP?= Content-Type: multipart/alternative; boundary=0023540103b6d2121504a4c7c894 Date: Fri, 3 Jun 2011 14:11:21 +0900 MIME-Version: 1.0 Sent to CCL by: =?EUC-KR?B?vK3H9sDP?= [fanmusic1- -gmail.com] --0023540103b6d2121504a4c7c894 Content-Type: text/plain; charset=ISO-8859-1 Is there dump file named "core"? If there is dump file, then check limitation of your system. 2011/6/3 neeraj misra neerajmisra%hotmail.com > > Sent to CCL by: "neeraj misra" [neerajmisra]![hotmail.com] > Dear members, > The following is the input of a gaussian calculation and > also the output.Even after running for three days it has possibly got > stuck....any help to solve this would be appreciated. > INPUT: > > # polar opt(TIGHT,diis) freq > b3lyp/6-311++g(d,p)SCF(xqc,vshift=100,maxcycle=512) > > ABCD > > 0 1 > Br 5.35450 -1.05260 -0.03250 > O 2.31980 -1.65120 -0.04060 > N 0.68670 2.69940 0.05660 > N 1.51070 0.50300 0.00760 > N 3.01230 2.38740 0.04830 > N 5.34950 2.06700 0.03600 > N -4.16190 -3.51580 -0.06830 > N -6.02390 1.65680 0.04720 > C 0.99300 -2.03300 -0.04620 > C 0.33640 -2.19520 -1.25680 > C 0.34110 -2.24720 1.15860 > C -1.00410 -2.58080 -1.26250 > C -0.99940 -2.63300 1.15290 > C -1.67190 -2.79970 -0.05770 > C 1.03450 -1.96540 -2.55670 > C 1.04420 -2.07350 2.46460 > C 2.58870 -0.30820 -0.01220 > C 1.78820 1.82210 0.03710 > C -0.70710 2.48280 0.05400 > C 3.89120 0.14720 -0.00340 > C 4.04410 1.51840 0.02740 > C -1.55810 3.42210 -0.52860 > C -1.23450 1.32970 0.63510 > C -2.93650 3.20810 -0.53000 > C -2.61280 1.11570 0.63360 > C -3.46380 2.05500 0.05110 > C -3.04530 -3.19470 -0.06350 > C -4.87580 1.83540 0.04890 > H -1.52990 -2.70860 -2.20660 > H -1.52170 -2.80100 2.09260 > H 0.47350 -2.39040 -3.39610 > H 1.15330 -0.89280 -2.73970 > H 2.02010 -2.44280 -2.56130 > H 0.48460 -2.53110 3.28770 > H 2.02820 -2.55370 2.44580 > H 1.16710 -1.00980 2.69170 > H 0.95950 3.67070 -0.05960 > H -1.15940 4.32420 -0.98540 > H -0.61420 0.60330 1.14640 > H -3.58690 3.94930 -0.98830 > H -3.01060 0.21830 1.10160 > H 6.09980 1.51390 0.43120 > H 5.42630 3.07600 0.06720 > > > OUTPUT > Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. > Requested convergence on MAX density matrix=1.00D-06. > Requested convergence on energy=1.00D-06. > Virtual orbitals will be shifted by 0.100 hartree. > No special actions if energy rises.> > > --0023540103b6d2121504a4c7c894 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Is there=A0dump file named "core"?
=A0
I= f there is dump file, then check limitation of your system.

2011/6/3 neeraj misra neerajmisra%hotmail.com <owner-chemistry(_)ccl.net>

Sent to CCL by: "neeraj =A0misra" [neerajmisra]![hotmail.com]
Dear members,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 The following is the input of a gaussian c= alculation and also the output.Even after running for three days it has pos= sibly got stuck....any help to solve this =A0would be appreciated.
INPUT:

=A0# polar opt(TIGHT,diis) freq b3lyp/6-311++g(d,p)SCF(xqc,vshift=3D100,max= cycle=3D512)

ABCD

0 =A01
Br =A0 =A0 =A0 =A0 =A05.35450 =A0 =A0 =A0 =A0-1.05260 =A0 =A0 =A0 =A0-0.032= 50
O =A0 =A0 =A0 =A0 =A0 2.31980 =A0 =A0 =A0 =A0-1.65120 =A0 =A0 =A0 =A0-0.040= 60
N =A0 =A0 =A0 =A0 =A0 0.68670 =A0 =A0 =A0 =A0 2.69940 =A0 =A0 =A0 =A0 0.056= 60
N =A0 =A0 =A0 =A0 =A0 1.51070 =A0 =A0 =A0 =A0 0.50300 =A0 =A0 =A0 =A0 0.007= 60
N =A0 =A0 =A0 =A0 =A0 3.01230 =A0 =A0 =A0 =A0 2.38740 =A0 =A0 =A0 =A0 0.048= 30
N =A0 =A0 =A0 =A0 =A0 5.34950 =A0 =A0 =A0 =A0 2.06700 =A0 =A0 =A0 =A0 0.036= 00
N =A0 =A0 =A0 =A0 =A0-4.16190 =A0 =A0 =A0 =A0-3.51580 =A0 =A0 =A0 =A0-0.068= 30
N =A0 =A0 =A0 =A0 =A0-6.02390 =A0 =A0 =A0 =A0 1.65680 =A0 =A0 =A0 =A0 0.047= 20
C =A0 =A0 =A0 =A0 =A0 0.99300 =A0 =A0 =A0 =A0-2.03300 =A0 =A0 =A0 =A0-0.046= 20
C =A0 =A0 =A0 =A0 =A0 0.33640 =A0 =A0 =A0 =A0-2.19520 =A0 =A0 =A0 =A0-1.256= 80
C =A0 =A0 =A0 =A0 =A0 0.34110 =A0 =A0 =A0 =A0-2.24720 =A0 =A0 =A0 =A0 1.158= 60
C =A0 =A0 =A0 =A0 =A0-1.00410 =A0 =A0 =A0 =A0-2.58080 =A0 =A0 =A0 =A0-1.262= 50
C =A0 =A0 =A0 =A0 =A0-0.99940 =A0 =A0 =A0 =A0-2.63300 =A0 =A0 =A0 =A0 1.152= 90
C =A0 =A0 =A0 =A0 =A0-1.67190 =A0 =A0 =A0 =A0-2.79970 =A0 =A0 =A0 =A0-0.057= 70
C =A0 =A0 =A0 =A0 =A0 1.03450 =A0 =A0 =A0 =A0-1.96540 =A0 =A0 =A0 =A0-2.556= 70
C =A0 =A0 =A0 =A0 =A0 1.04420 =A0 =A0 =A0 =A0-2.07350 =A0 =A0 =A0 =A0 2.464= 60
C =A0 =A0 =A0 =A0 =A0 2.58870 =A0 =A0 =A0 =A0-0.30820 =A0 =A0 =A0 =A0-0.012= 20
C =A0 =A0 =A0 =A0 =A0 1.78820 =A0 =A0 =A0 =A0 1.82210 =A0 =A0 =A0 =A0 0.037= 10
C =A0 =A0 =A0 =A0 =A0-0.70710 =A0 =A0 =A0 =A0 2.48280 =A0 =A0 =A0 =A0 0.054= 00
C =A0 =A0 =A0 =A0 =A0 3.89120 =A0 =A0 =A0 =A0 0.14720 =A0 =A0 =A0 =A0-0.003= 40
C =A0 =A0 =A0 =A0 =A0 4.04410 =A0 =A0 =A0 =A0 1.51840 =A0 =A0 =A0 =A0 0.027= 40
C =A0 =A0 =A0 =A0 =A0-1.55810 =A0 =A0 =A0 =A0 3.42210 =A0 =A0 =A0 =A0-0.528= 60
C =A0 =A0 =A0 =A0 =A0-1.23450 =A0 =A0 =A0 =A0 1.32970 =A0 =A0 =A0 =A0 0.635= 10
C =A0 =A0 =A0 =A0 =A0-2.93650 =A0 =A0 =A0 =A0 3.20810 =A0 =A0 =A0 =A0-0.530= 00
C =A0 =A0 =A0 =A0 =A0-2.61280 =A0 =A0 =A0 =A0 1.11570 =A0 =A0 =A0 =A0 0.633= 60
C =A0 =A0 =A0 =A0 =A0-3.46380 =A0 =A0 =A0 =A0 2.05500 =A0 =A0 =A0 =A0 0.051= 10
C =A0 =A0 =A0 =A0 =A0-3.04530 =A0 =A0 =A0 =A0-3.19470 =A0 =A0 =A0 =A0-0.063= 50
C =A0 =A0 =A0 =A0 =A0-4.87580 =A0 =A0 =A0 =A0 1.83540 =A0 =A0 =A0 =A0 0.048= 90
H =A0 =A0 =A0 =A0 =A0-1.52990 =A0 =A0 =A0 =A0-2.70860 =A0 =A0 =A0 =A0-2.206= 60
H =A0 =A0 =A0 =A0 =A0-1.52170 =A0 =A0 =A0 =A0-2.80100 =A0 =A0 =A0 =A0 2.092= 60
H =A0 =A0 =A0 =A0 =A0 0.47350 =A0 =A0 =A0 =A0-2.39040 =A0 =A0 =A0 =A0-3.396= 10
H =A0 =A0 =A0 =A0 =A0 1.15330 =A0 =A0 =A0 =A0-0.89280 =A0 =A0 =A0 =A0-2.739= 70
H =A0 =A0 =A0 =A0 =A0 2.02010 =A0 =A0 =A0 =A0-2.44280 =A0 =A0 =A0 =A0-2.561= 30
H =A0 =A0 =A0 =A0 =A0 0.48460 =A0 =A0 =A0 =A0-2.53110 =A0 =A0 =A0 =A0 3.287= 70
H =A0 =A0 =A0 =A0 =A0 2.02820 =A0 =A0 =A0 =A0-2.55370 =A0 =A0 =A0 =A0 2.445= 80
H =A0 =A0 =A0 =A0 =A0 1.16710 =A0 =A0 =A0 =A0-1.00980 =A0 =A0 =A0 =A0 2.691= 70
H =A0 =A0 =A0 =A0 =A0 0.95950 =A0 =A0 =A0 =A0 3.67070 =A0 =A0 =A0 =A0-0.059= 60
H =A0 =A0 =A0 =A0 =A0-1.15940 =A0 =A0 =A0 =A0 4.32420 =A0 =A0 =A0 =A0-0.985= 40
H =A0 =A0 =A0 =A0 =A0-0.61420 =A0 =A0 =A0 =A0 0.60330 =A0 =A0 =A0 =A0 1.146= 40
H =A0 =A0 =A0 =A0 =A0-3.58690 =A0 =A0 =A0 =A0 3.94930 =A0 =A0 =A0 =A0-0.988= 30
H =A0 =A0 =A0 =A0 =A0-3.01060 =A0 =A0 =A0 =A0 0.21830 =A0 =A0 =A0 =A0 1.101= 60
H =A0 =A0 =A0 =A0 =A0 6.09980 =A0 =A0 =A0 =A0 1.51390 =A0 =A0 =A0 =A0 0.431= 20
H =A0 =A0 =A0 =A0 =A0 5.42630 =A0 =A0 =A0 =A0 3.07600 =A0 =A0 =A0 =A0 0.067= 20


OUTPUT
Requested convergence on RMS density matrix=3D1.00D-08 within 128 cycles. =A0Requested convergence on MAX density matrix=3D1.00D-06.
=A0Requested convergence on =A0 =A0 =A0 =A0 =A0 =A0 energy=3D1.00D-06.
=A0Virtual orbitals will be shifted by =A0 0.100 hartree.
=A0No special actions if energy rises.



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--0023540103b6d2121504a4c7c894-- From owner-chemistry@ccl.net Fri Jun 3 12:41:00 2011 From: "Marcel Swart marcel.swart a icrea.cat" To: CCL Subject: CCL: Popularity poll density functionals 2011 Message-Id: <-44832-110603123618-32321-Y43T7QKpP4tzckOQKIuedQ=-=server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 3 Jun 2011 18:36:03 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Marcel Swart [marcel.swart*o*icrea.cat] Dear all, similar to last year, we have opened an online popularity poll for density functionals. This popularity poll is based on an idea by Miquel Duran after a seminar given by Matthias Bickelhaupt (see http://www.marcelswart.eu/dft-poll/newsitem.pdf). By choice only 20 density functionals are given in the Primera Divisió, 10 in the Segona Divisió with 20 reserve places available (in Segona Divisió) for additional suggestions (mail these to marcel.swart (at) udg.edu). The functionals are ordered alphabetically (except for the reserve places that are ordered chronologically).Please indicate for both the Primera Divisió and the Segona Divisió what you think of current density functionals. The poll will be open until Oct. 1 2011, after which the ranking of density functionals for the year 2011 will be made. http://www.marcelswart.eu/dft-poll/2011.html Note that last year's ranking can be found in the news-item: http://www.marcelswart.eu/dft-poll/newsitem.pdf Marcel Swart Matthias Bickelhaupt Miquel Duran =================================== dr. Marcel Swart ICREA Research Professor at Institut de Química Computacional Universitat de Girona Facultat de Ciències Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart-$-icrea.cat marcel.swart-$-udg.edu web http://www.marcelswart.eu =================================== From owner-chemistry@ccl.net Fri Jun 3 13:15:01 2011 From: "Juan C. Drosos jdrosos,gmail.com" To: CCL Subject: CCL:G: How to install gaussian 09 in Open suse 11.4? Message-Id: <-44833-110603124555-10506-TA/flhChCzMQ2xt7FjGEXA..server.ccl.net> X-Original-From: "Juan C. Drosos" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 3 Jun 2011 11:45:45 -0500 MIME-Version: 1.0 Sent to CCL by: "Juan C. Drosos" [jdrosos*gmail.com] First of all you will need a valid license for Gaussian09 and then ask technical support with gaussian team. That would be the easiest way Best Regards Juan C Drosos. On Thu, Jun 2, 2011 at 9:48 AM, Jorl Jose Montalvo montalvo161-,-hotmail.com wrote: > > Sent to CCL by: "Jorl Jose Montalvo" [montalvo161 . hotmail.com] > Dear community. > > I have tried to install gaussian 09 on suse 11.4 in accordance with the instructions provided by the G09's main page but I could not do exactly .... I had problems with the files  .login and .profile, which does not encounter in open suse. > Could someone tell me an G09 installation manual for suse 11.4? or where files (.login and .profile) are located in suse 11.4?>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Fri Jun 3 14:24:00 2011 From: "Markus Dittrich dittrich#psc.edu" To: CCL Subject: CCL: Request for Proposals for Simulation Time on Anton at NRBSC/PSC Message-Id: <-44834-110603092013-25419-+KPFZiRA9fP0qSCOfS6bQw|-|server.ccl.net> X-Original-From: "Markus Dittrich" Date: Fri, 3 Jun 2011 09:20:10 -0400 Sent to CCL by: "Markus Dittrich" [dittrich+/-psc.edu] Dear Colleagues, The National Resource for Biomedical Supercomputing (NRBSC) is soliciting proposals for computer time on Anton, a special-purpose supercomputer for molecular dynamics (MD) simulation designed by D.E. Shaw Research (DESRES). A 512-node Anton machine is currently available and in production use at NRBSC at the Pittsburgh Supercomputing Center (PSC). The machine has been made available without cost by DESRES for non-commercial research use by universities and other not-for-profit institutions and is hosted by NRBSC with funding from the National Institute of General Medical Sciences under grant RC2GM093307. This RFP solicits proposals for an extension period beyond the originally planned project duration. To qualify for an allocation on Anton, the principal investigator must be a faculty or staff member at a U.S. academic or non-profit research institution. For more details regarding proposal submission please go to If you have questions please contact grants:-:psc.edu. With best regards, NRBSC From owner-chemistry@ccl.net Fri Jun 3 22:49:00 2011 From: "Jonas Baltrusaitis jasius_1]![yahoo.com" To: CCL Subject: CCL:G: How to build a linux cluster for computational chemistry purposes?, HELP Message-Id: <-44835-110603170300-18373-T+Nwv5iGwiCuGP7BH5+Fkg/./server.ccl.net> X-Original-From: Jonas Baltrusaitis Content-Type: multipart/alternative; boundary="0-1494922662-1307134972=:58655" Date: Fri, 3 Jun 2011 14:02:52 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Jonas Baltrusaitis [jasius_1[*]yahoo.com] --0-1494922662-1307134972=:58655 Content-Type: text/plain; charset=us-ascii Use Rocks cluster Jonas ________________________________ > From: Jun Zhang coolrainbow]*[yahoo.cn To: "Baltrusaitis, Jonas " Sent: Thu, June 2, 2011 9:31:02 PM Subject: CCL:G: How to build a linux cluster for computational chemistry purposes?, HELP Hi Miguel Quiliano: I had ever written a very detailed document on cluster building, but it was written in Chinese rather than in English so I don't know whether it can help you... If you need it, I can send you by e-mail. Good Luck! Jun Zhang Nankai University coolrainbow(_)yahoo.cn > >Dear community. > >After... talk.. and talk.. with my boss, I convinced him to build a linux >cluster for computational chemistry purposes, in other words... to use >Gaussian03. So now I have 80 cores at my disposal. We also have TCP/LINDA. > >Could you please recommend me, one operative system and some online guide to >build it or book? Personal experiences are welcome. > >Thanks in advance. > >Miguel Quiliano. > --0-1494922662-1307134972=:58655 Content-Type: text/html; charset=us-ascii
Use Rocks cluster

Jonas


From: Jun Zhang coolrainbow]*[yahoo.cn <owner-chemistry(0)ccl.net>
To: "Baltrusaitis, Jonas " <jasius_1(0)yahoo.com>
Sent: Thu, June 2, 2011 9:31:02 PM
Subject: CCL:G: How to build a linux cluster for computational chemistry purposes?, HELP

Hi Miguel Quiliano:
 
     I had ever written a very detailed document on cluster building, but it was written in Chinese rather than in English so I don't know whether it can help you... If you need it, I can send you by e-mail.
 
Good Luck!

Jun Zhang
Nankai University
coolrainbow(_)yahoo.cn


Dear community.

After... talk.. and talk.. with my boss, I convinced him to build a linux cluster for computational chemistry purposes, in other words... to use Gaussian03. So now I have 80 cores at my disposal. We also have TCP/LINDA.

Could you please recommend me, one operative system and some online guide to build it or book? Personal experiences are welcome.

Thanks in advance.

Miguel Quiliano.
--0-1494922662-1307134972=:58655-- From owner-chemistry@ccl.net Fri Jun 3 23:24:00 2011 From: "David A Mannock dmannock%ualberta.ca" To: CCL Subject: CCL:G: How to install gaussian 09 in Open suse 11.4? Message-Id: <-44836-110603154555-30028-eSc6C2yCCSce8pLLLmWjCA],[server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=20cf3071c9fe06a82704a4d40063 Date: Fri, 3 Jun 2011 13:45:47 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock::ualberta.ca] --20cf3071c9fe06a82704a4d40063 Content-Type: text/plain; charset=ISO-8859-1 Here's my 2 cents worth. After a false start with RedHat 5.3, which was incredible clumsy, I chose Ubuntu 10.04 as the OS as it was far more user friendly. My university has a site license for g09 and I asked someone at research computer support to remotely install a compiled copy of g09. All that needed was updates to the environmental variables to change over from g03. Dave On Fri, Jun 3, 2011 at 10:45 AM, Juan C. Drosos jdrosos,gmail.com < owner-chemistry[]ccl.net> wrote: > > Sent to CCL by: "Juan C. Drosos" [jdrosos*gmail.com] > First of all you will need a valid license for Gaussian09 and then ask > technical support with gaussian team. > That would be the easiest way > Best Regards > > Juan C Drosos. > > On Thu, Jun 2, 2011 at 9:48 AM, Jorl Jose Montalvo > montalvo161-,-hotmail.com wrote: > > > > Sent to CCL by: "Jorl Jose Montalvo" [montalvo161 . hotmail.com] > > Dear community. > > > > I have tried to install gaussian 09 on suse 11.4 in accordance with the > instructions provided by the G09's main page but I could not do exactly .... > I had problems with the files .login and .profile, which does not encounter > in open suse. > > Could someone tell me an G09 installation manual for suse 11.4? or where > files (.login and .profile) are located in suse 11.4?> > > --20cf3071c9fe06a82704a4d40063 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Here's my 2 cents worth. After a false start with RedHat 5.3, which was= incredible clumsy, I chose Ubuntu 10.04 as the OS as it was far more user = friendly. My university has a site license for g09 and I asked someone at r= esearch computer support to remotely install a compiled copy of g09. All th= at needed was updates to the environmental variables to change over from g0= 3. Dave

On Fri, Jun 3, 2011 at 10:45 AM, Juan C. Dro= sos jdrosos,gmail.com &l= t;owner-chemistry[]ccl.net>= ; wrote:

Sent to CCL by: "Juan C. Drosos" [jdrosos*gmail.com]
First of all you will need a valid license for Gaussian09 and then ask
technical support with gaussian team.
That would be the easiest way
Best Regards

Juan C Drosos.

On Thu, Jun 2, 2011 at 9:48 AM, Jorl Jose Montalvo
montalvo161-,-hotmail.com<= /a> <owner-chemistry[*]ccl.= net> wrote:
>
> Sent to CCL by: "Jorl Jose Montalvo" [montalvo161 . hotmail.com]
> Dear community.
>
> I have tried to install gaussian 09 on suse 11.4 in accordance with th= e instructions provided by the G09's main page but I could not do exact= ly .... I had problems with the files =A0.login and .profile, which does no= t encounter in open suse.
> Could someone tell me an G09 installation manual for suse 11.4? or whe= re files (.login and .profile) are located in suse 11.4?> =A0 =A0 =A0=> =A0 =A0 =A0http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.c= cl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt&= gt;
>
>



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