From owner-chemistry@ccl.net Wed Oct 23 01:27:00 2013 From: "John Keller jwkeller..alaska.edu" To: CCL Subject: CCL: molecular orbitals using NWChem Message-Id: <-49264-131023012558-14178-0DuxoG6Ps6N+0SEu3wbymg-#-server.ccl.net> X-Original-From: John Keller Content-Type: multipart/alternative; boundary=047d7bd8fc202be25204e961c0c1 Date: Tue, 22 Oct 2013 21:25:51 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller!=!alaska.edu] --047d7bd8fc202be25204e961c0c1 Content-Type: text/plain; charset=ISO-8859-1 Hi Surinder, One way to do this is to use the Guest account on the WebMO website ( www.webmo.net) to visualize NWchem-generated MOs. This account has a CPU time limit of 60 sec, which is plenty of time for this task - since the surface computation is done by JAVA on your local machine. For example I ran an MO job on my local copy of NWChem 6.1 using the following input.in file. Then I uploaded the resulting output.out file (780 KB) to the WebMO website (www.webmo.net) (do New Job, Import Job, Filetype NWChem), and clicked the View icon to the right of MO #9. See job 138684. (BTW, I am afraid the free version of WebMO, which can be downloaded and installed on your local machine, does not display surfaces....) Best, John Keller, Univ of Alaska Fairbanks title "HCO2H-631GsB3LYP-MO" echo charge 0 geometry C 0.00000000 0.00000000 0.00000000 O -0.41455000 -1.28193900 0.00000000 H -1.39174200 -1.25943900 0.00000000 O -0.72264400 0.96391400 0.00000000 H 1.09928900 0.02736700 0.00000000 end basis print * library 6-31G* end dft print "final vectors" high XC b3lyp mult 1 end task dft energy property dipole mulliken end task dft property On Tue, Oct 22, 2013 at 6:30 AM, Surinder pal kaur simmi.msc7++gmail.com < owner-chemistry]~[ccl.net> wrote: > > Sent to CCL by: "Surinder pal kaur" [simmi.msc7++gmail.com] > Dear CCL members, > Can anyone please guide me how to plot molecular orbitals using NWChem and > about freely available visualization softwares used for this purpose. > > Thanking You. > > Surinder Pal Kaur> > > --047d7bd8fc202be25204e961c0c1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Surinder,
One way to do th= is is to use the Guest account on the WebMO website (www.webmo.net) to visualize NWchem-generated MOs. This accou= nt has a CPU time limit of 60 sec, which is plenty of time for this task - = since the surface computation is done by JAVA on your local machine.
For example I ran an MO job on my local copy of NWChem 6.1 using the follow= ing input.in file. Then I uploaded the resu= lting output.out file (780 KB) to the WebMO website (www.webmo.net) (do New Job, Import Job, Filetype NWChem), an= d clicked the View icon to the right of MO #9. See job 138684.
(BTW, I am afraid the free version of WebMO, which can be downloaded and in= stalled on your local machine, does not display surfaces....)
Best= ,
John Keller, Univ of Alaska Fairbanks

title "HCO2H-631GsB3LYP-MO"

echo

charge 0<= br>
geometry
C 0.00000000 0.00000000 0.00000000
O -0.41455000 -1.2= 8193900 0.00000000
H -1.39174200 -1.25943900 0.00000000
O -0.72264400= 0.96391400 0.00000000
H 1.09928900 0.02736700 0.00000000
end

basis print
=A0* librar= y 6-31G*
end

dft
=A0print "final vectors" high
= =A0XC b3lyp
=A0mult 1
end
task dft energy

property
=A0 d= ipole
=A0 mulliken
end
task dft property



On Tue, Oc= t 22, 2013 at 6:30 AM, Surinder pal kaur simmi.msc7++gmail.com <owner-chemistry]~[ccl.net> wrote:<= br>

Sent to CCL by: "Surinder pal kaur" [simmi.msc7++gmail.com]
Dear CCL members,
Can anyone please guide me how to plot molecular orbitals using NWChem and = about freely available visualization softwares used for this purpose.

Thanking You.

Surinder Pal Kaur



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--047d7bd8fc202be25204e961c0c1-- From owner-chemistry@ccl.net Wed Oct 23 03:36:00 2013 From: "Shilpi V shilpigre]*[gmail.com" To: CCL Subject: CCL: Problem with running Large files (2GB limit) using Nwchem 6.0 Message-Id: <-49265-131023031857-28930-LsIH1fyhEAZQHOwO/iPUmg ~~ server.ccl.net> X-Original-From: "Shilpi V" Date: Wed, 23 Oct 2013 03:18:56 -0400 Sent to CCL by: "Shilpi V" [shilpigre[-]gmail.com] Dear all, I am trying to perform a frequency calculation on a large system(with 60 atoms in total) using nwchem-6.0-binary-redhat-5-5-gcc-4-1-2 in a work station with 2 cpus, x86_64, 32GB RAM. I specified the memory of 15000 mb as memory total 15000 mb stack 3750 mb heap 3750 mb global 7500 mb and the job terminated giving the following error Last System Error Message from Task 0:: Numerical result out of range 0:armci_malloc:malloc 1 failed: 1937664008 (rank:0 hostname:fullerene pid:2418):ARMCI DASSERT fail. memory.c:PARMCI_Malloc():872 cond:0 0: ARMCI aborting 0 (0). 0: ARMCI aborting 0 (0). system error message: Invalid argument Is it the problem of binary version of nwchem not working for large files(2GB limit)? Is there any way we can use the binary version of nwchem for running frequency calculations for such large files? Or Is there any other way u can suggest to finish my calculation successfully.?? Please help me to find the solution for this problem. Regards, V.Shilpi From owner-chemistry@ccl.net Wed Oct 23 12:01:01 2013 From: "Jeya vimalan jeyavimalan2k()gmail.com" To: CCL Subject: CCL: Bond variations from the trajectory Message-Id: <-49266-131023092605-17040-xh3hOv/sIgYgiUQ1f7EwCQ.:.server.ccl.net> X-Original-From: Jeya vimalan Content-Type: multipart/alternative; boundary=047d7b10c9cb810bd104e9687437 Date: Wed, 23 Oct 2013 15:25:47 +0200 MIME-Version: 1.0 Sent to CCL by: Jeya vimalan [jeyavimalan2k|-|gmail.com] --047d7b10c9cb810bd104e9687437 Content-Type: text/plain; charset=ISO-8859-1 Dear Lammps Users, I have a molecular dynamics simulation done for a system where part of the molecule undergoes elongation during the simulation window and other remains same or decreased. I would like to address this effect quantitatively to bring out the possible reason of why this occurs. For example, I can calculate the bond length for each structure in the trajectory, through which possibly the standard deviation that provides an estimate of the relative variations of the bond in the system. But this is going to be a hard procedure. Does any one have some ideas how this observation can be well presented. If so can you please share me your views. Thanks in advance. Vimala --047d7b10c9cb810bd104e9687437 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Lammps Users,

I have a molecular dyna= mics simulation done for a system
where part of the molecule unde= rgoes elongation during the simulation
window and other remains same or decreased.

=
I would like to = address this effect quantitatively to
bring out the possible reason of why this occurs.

For example, I can calculate the bond leng= th for each structure
in the trajector= y, through which possibly the standard deviation that provides
an estimate of the rela= tive variations of the bond in the system.

But this is going to be a hard procedure.
<= div style=3D"font-family:arial,sans-serif;font-size:13px">Does any one have= some ideas how this observation
can be well pres= ented.
If so can you please share me your views.

<= div>Thanks in advance.
Vimala
--047d7b10c9cb810bd104e9687437-- From owner-chemistry@ccl.net Wed Oct 23 18:08:01 2013 From: "Raul Alvarez ralvarez\a/chemcomp.com" To: CCL Subject: CCL: CCG releases MOE 2013.08 with EHT for Pharmacophore Discovery Message-Id: <-49267-131023180515-16141-Mq1Mdq8sq5MgWcUTJHqT/A|a|server.ccl.net> X-Original-From: "Raul Alvarez" Date: Wed, 23 Oct 2013 18:05:14 -0400 Sent to CCL by: "Raul Alvarez" [ralvarez[A]chemcomp.com] We are pleased to announce the 2013 release of the Molecular Operating Environment (MOE). MOE version 2013.08 introduces a new pharmacophore scheme based on Extended Hckel Theory, biologics applications for de novo and knowledge-based loop and linker modeling as well as enhancements in water placement for solvent analysis. Select core system developments in MOE 2013.08 include 64-bit support and system manager grouping hierarchy for project data. For additional information or to request a free trial of MOE 2013.08, please contact: Raul Alvarez, Sr. Marketing Manager () ralvarez() chemcomp.com =============================================================== NEW & ENHANCED FEATURES IN MOE 2013.08 =============================================================== *Extended Hckel Theory for Pharmacophore Discovery - Apply EHT strengths to identify and discover weak and strong interactions - Annotate non-standard interactions: halogen and CH bond donors - Score pharmacophore hits using sum of interaction energies *de novo Loop and Linker Modeler - Search and browse for de novo and knowledge-based loop candidates - Generate multiple loop conformations and score loop-loop interactions - Investigate linkers for fusion proteins and dual variable domains *Protein Alignments and Superpositions - Superpose protein structures independent of sequence - Apply new threading methodology for sequence to structure alignments - Align sequences and superpose structures using STOVCA criteria *Core System Enhancements (with 64-bit support) - Create additional data grouping level in System Manager - Handle large number of protein:ligand complexes in real-time - Color database viewer text and cells by data values for enhanced analysis *Interface to Mogul from CCDC - Access a knowledge-based library of small molecule crystallographic data - Visualize histograms and statistics for bond angles, dihedrals and torsions - Ensure ligand conformation is consistent with the CSD *Solvent Analysis using 3D-RISM Enhancements - Calculate water densities on full protein or protein:protein interface - Accurate placement and stability prediction of water sites - Use 3D-RISM densities to validate water position in crystal structures ================================================================ >> Key application areas in MOE: http://www.chemcomp.com/software.htm Structure-Based Design - Fragment-Based Design - Pharmacophore Discovery - Medicinal Chemistry Applications - Biologics Applications - Protein and Antibody Modeling - Molecular Modeling and Simulations - Cheminformatics & QSAR ================================================================ Read/download the official MOE 2013.08 press release () http://www.chemcomp.com/press_releases/2013-10-23-MOE2013.08.pdf Raul Alvarez Senior Marketing Manager Chemical Computing Group T. + 1 (514) 393-1055 x 134 | F. +1 (514) 874-9538 ralvarez() chemcomp.com | www.chemcomp.com