From owner-chemistry@ccl.net Fri Nov 21 07:06:00 2014 From: "Jan Jensen jhjensen**chem.ku.dk" To: CCL Subject: CCL: Introducing Computational Chemistry Daily Message-Id: <-50770-141121041726-21554-A/s1ELkdnl9CMgxgmlj1EQ__server.ccl.net> X-Original-From: "Jan Jensen" Date: Fri, 21 Nov 2014 04:17:21 -0500 Sent to CCL by: "Jan Jensen" [jhjensen]~[chem.ku.dk] Computational Chemistry Daily (http://tinyurl.com/compchemdaily) aggregates posts related to computational chemistry on social media such as Twitter, Google+ and Facebook on a daily basis. It identifies the posts by certain words or hashtags such as #compchem and everyone can contribute. Hope you find it useful. Best regards, Jan Jensen From owner-chemistry@ccl.net Fri Nov 21 07:40:00 2014 From: "David A Case case ~~ biomaps.rutgers.edu" To: CCL Subject: CCL: Nanotubes with Amber (GAFF) ff in GROMACS Message-Id: <-50771-141120074849-1339-7JRjLReO2vw3qDG3t5Oaqw-.-server.ccl.net> X-Original-From: David A Case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 20 Nov 2014 07:48:43 -0500 Mime-Version: 1.0 Sent to CCL by: David A Case [case-$-biomaps.rutgers.edu] On Thu, Nov 20, 2014, Sergio Manzetti sergio.manzetti%%outlook.com wrote: > > Does anyone know of a tutorial that explains the procedure to generate > non-periodic *gro, *top and *itp files for the GAFF force field in > GROMACS 5.0+ ? There are a couple of ways to use Amber force field parameters in Gromacs. See the links "Using the Amber force field in GROMACS" at this site: http://ambermd.org However, as one of the people who contributed to the development of the GAFF force field, I feel obliged to point out that we never considered nanotubes when developing these parameters. So please proceed with caution, and take account of what others have learned from simulations of these sorts of systems. ...dave case From owner-chemistry@ccl.net Fri Nov 21 08:15:00 2014 From: "Nico Green nicogreen6(0)gmail.com" To: CCL Subject: CCL: Opt Message-Id: <-50772-141121075622-16124-cT1eOgwQ1A7GFR7jIshjTA()server.ccl.net> X-Original-From: Nico Green Content-Type: multipart/alternative; boundary=089e011762957cd01505085df84a Date: Fri, 21 Nov 2014 09:56:17 -0300 MIME-Version: 1.0 Sent to CCL by: Nico Green [nicogreen6()gmail.com] --089e011762957cd01505085df84a Content-Type: text/plain; charset=UTF-8 Dear CCLers I'm trying to find a complex in the reaction coordinate. I have previously find it for another system, the difference now is that this new structure has an ester group instead of a carboxylic acid. The system is about 50 atoms. I have found the complex at B3LYP/6-31G*, now im trying to find it at B3LYP/6-311+G**, however i've have try and try with no luck. My normal methodology is that i run an IRC and two options: It ends on the complex or the path has a shoulder and the reoptimization of that point gives me the structure im looking for. However at this new level of theory, this metodology is not working. The reoptimization of the previously found complex goes to reactants, and the IRC of the newly generated TSs give me the reactants or in some cases a shoulder, where the re reoptimization give me the reactants. I just use opt(CalcFc,Noeigentest) for optimization of the complex. I'm thinking adding tight and fixing the key distance of the complex in the reaction. Any suggestions or you think that's a good option? Thank you all Nico --089e011762957cd01505085df84a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear CCLers

I'm trying to find a co= mplex in the reaction coordinate.=C2=A0

I have pre= viously find it for another system, the difference now is that this new str= ucture has an ester group instead of a carboxylic acid.
=C2=A0
The system is about 50 atoms.

I have found= the complex at B3LYP/6-31G*, now im trying to find it at B3LYP/6-311+G**, = however i've have try and try with no luck.

My= normal methodology is that i run an IRC and two options:
It ends= on the complex or the path has a shoulder and the reoptimization of that p= oint gives me the structure im looking for.=C2=A0

= However at this new level of theory, this metodology is not working.=C2=A0<= /div>

The reoptimization of the previously found complex= goes to reactants, and the IRC of the newly generated TSs give me the reac= tants or in some cases a shoulder, where the re reoptimization give me the = reactants.

I just use opt(CalcFc,Noeigentest) for = optimization of the complex.

I'm thinking addi= ng tight and fixing the key distance of the complex in the reaction.
<= div>
Any suggestions or you think that's a good option?

Thank you all

Nico
--089e011762957cd01505085df84a-- From owner-chemistry@ccl.net Fri Nov 21 09:32:01 2014 From: "Marcel Swart marcel.swart]~[icrea.cat" To: CCL Subject: CCL: Nanotubes with Amber (GAFF) ff in GROMACS Message-Id: <-50773-141121093101-28440-mxi/Wp1lVFRRLrYvvOKPhw|server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Fri, 21 Nov 2014 15:30:49 +0100 Mime-Version: 1.0 (Mac OS X Mail 8.1 \(1993\)) Sent to CCL by: Marcel Swart [marcel.swart===icrea.cat] Sílvia Osuna, Ken Houk and co-workers have used GAFF for nanotubes: ACS Nano, 2013, 7 (3), pp 2659–2668 http://pubs.acs.org/doi/full/10.1021/nn4000435 (also have a look at the SuppInfo tor the movies they made, with spiders and lizzards: http://spin.udg.edu/iqc/?p=1346) Marcel > On 20 Nov 2014, at 13:48 , David A Case case ~~ biomaps.rutgers.edu wrote: > > > Sent to CCL by: David A Case [case-$-biomaps.rutgers.edu] > On Thu, Nov 20, 2014, Sergio Manzetti sergio.manzetti%%outlook.com wrote: >> >> Does anyone know of a tutorial that explains the procedure to generate >> non-periodic *gro, *top and *itp files for the GAFF force field in >> GROMACS 5.0+ ? > > There are a couple of ways to use Amber force field parameters in Gromacs. > See the links "Using the Amber force field in GROMACS" at this site: > > http://ambermd.org > > However, as one of the people who contributed to the development of the GAFF > force field, I feel obliged to point out that we never considered nanotubes > when developing these parameters. So please proceed with caution, and take > account of what others have learned from simulations of these sorts of > systems. > > ...dave case =================================== Prof. Dr. Marcel Swart ICREA Research Professor at Institut de Química Computacional i Catàlisi Universitat de Girona Facultat de Ciències Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart(0)icrea.cat marcel.swart(0)udg.edu web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =================================== From owner-chemistry@ccl.net Fri Nov 21 23:19:01 2014 From: "shawkat islam sislam|,|swin.edu.au" To: CCL Subject: CCL: ADF CIO_ERROR cio_llwrite: write failed Message-Id: <-50774-141121231644-6370-MuaDzMIs7QHSJJYYALGEcw.:.server.ccl.net> X-Original-From: "shawkat islam" Date: Fri, 21 Nov 2014 23:16:43 -0500 Sent to CCL by: "shawkat islam" [sislam##swin.edu.au] Hi CCLusers, I wanted to run a bulk optimiztion in ADF but got this error. Could you tell me how to overcome it? FunctionSetOverlapModule: use new routines 3 forrtl: No space left on device forrtl: No space left on device *************************************************************************** **** ADF EXIT called CIO_ERROR cio_llwrite: write failed (/tmp/kid_0.cto78U/SCRATCH28,fd=37,rec=1153) Thanks Shawkat