Re: [gmx-users] error estimates of free energy calculations

Berk Hess wrote: From: David Mobley [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] error estimates of free energy calculations Date: Tue, 15 May 2007 15:55:01 -0700

Re: [gmx-users] PBC problem

Hi Yuguang, Gromacs should automatically fix the box to meet the requirements during an mdrun with pressure coupling (but does sometimes fail). There is also a certain tolerance in gromacs for the deviations. Anyway.., you can download a version of GMX3.2.1 from

RE: [gmx-users] PBC problem

Hi Tsjerk, Thanks. I will try that. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original

[gmx-users] using VMD with GROMACS trajectories

sichuan xu wrote: Dear Mark and other friends£¬ In future, please change the subject of the email to something relevant, to improve your chances of getting a useful answer and avoid wasting people's time and effort. I am a new user of Gromacs. I can obtain .xtc, .top, and .log files. But

Re: [gmx-users] using VMD with GROMACS trajectories

Hi Mark, David was installing a new server - as soon as I get an IP for it I'll enter it in the gromacs DNS and we can put a wiki online :-) David - any update? Cheers, Erik On May 16, 2007, at 10:51 AM, Mark Abraham wrote: Mark Abraham wrote: Roughly speaking, a gromacs .top file has

[gmx-users] top

Dear all how can i create popc.top after run make-hole? Got a little couch potato? Check out fun summer activities for kids.

[gmx-users] Gromacs on Xserver G5 /MPI

Dear All, Does anyone have experience with running gromacs on a apple Xserve G5? A simple install works fine but when I try to run mdrun on 2 processors using mpi I get one process running at +/- 70% CPU and one remains at 0% CPU. Does this sound familiar to anyone? System: Xserve G5

Re: [gmx-users] Gromacs on Xserver G5 /MPI

abelius wrote: Dear All, Does anyone have experience with running gromacs on a apple Xserve G5? A simple install works fine but when I try to run mdrun on 2 processors using mpi I get one process running at +/- 70% CPU and one remains at 0% CPU. Does this sound familiar to anyone? System:

Re: [gmx-users] Gromacs on Xserver G5 /MPI

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Mpi version: mpich-1.2.6 I tested the same command on a linux-gentoo system with mpich-1.2.7 and it worked perfectly. I guess I should update the mpich first? This would be a lot of work since It would mean updating SGE also. Any ideas for easier

Re: [gmx-users] same simulation, different results

Thanks a lot--that was it. On May 15, 2007, at 12:42 PM, David van der Spoel wrote: Jim Fonseca wrote: Hi, Does anyone know what would cause a simulation to change if I run it a second time? I'm starting with an EM structure and just doing a quick 10 ps simulation. I've found that (in

Re: [gmx-users] same simulation, different results

Stéphane Téletchéa wrote: Jim Fonseca a écrit : Thanks a lot--that was it. On May 15, 2007, at 12:42 PM, David van der Spoel wrote: Furthermore for a real test case, i would use a monoprocessor run since nic interfaces and smp can introduces little artifacts (roundoffs) leading to

Re: [gmx-users] Gromacs on Xserver G5 /MPI

abelius wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Mpi version: mpich-1.2.6 I tested the same command on a linux-gentoo system with mpich-1.2.7 and it worked perfectly. I guess I should update the mpich first? This would be a lot of work since It would mean updating SGE also. Any

[gmx-users] compatibility of MOPAC charges with GROMACS ?

Dear all I'm trying to assemble a topology entry for S-nitrosocysteine. Searching through the examples in the PDB revealed quite a spread of bond lengths and angles - the N=O bond ranges from 1.2 to 1.47A, for example. To get more rigorously derived figures, and to calculate charges, I thought

[gmx-users] top

how can i create popc.top after run make-hole? search popc.top The answer is there. http://www.gromacs.org/external/search.html Make sure to click on the Mailing List radio button before the search. ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Error while doing EM in DMSO.

Dear Users, First of all thank you Mark, yes you are right. it was problem of force field and topoloy file mismatch. I have made changes in the ffG43a1 residue toplogy file for DMSO., but still getting the same error. Please let me know if i am doing some mistake. ***changes

Re: [gmx-users] Gromacs on Xserver G5 /MPI

MPICH-1.2.xx is not recommended for Mac OS X (Unless you are using MPICH-over-Myrinet). You'll run into all sorts of problems with MPICH-1, its much much slower too! Try using Open MPI, LAM/MPI, or MPICH-2. Warner Yuen Scientific Computing Consultant Apple Computer email: wyuen at

Re: [gmx-users] Error while doing EM in DMSO.

Anil Kumar wrote: Dear Users, First of all thank you Mark, yes you are right. it was problem of force field and topoloy file mismatch. I have made changes in the ffG43a1 residue toplogy file for DMSO., but still getting the same error. Please let me know if i am doing some mistake. If the

[gmx-users] SGI Altix stack traceback

Hi All, the 3.3.1 version of gromacs was installed on A SGI Altix 3700 BX2. When I run mdrun_mpi_f using 8 processors for a ~500k atoms system, i receive the follwing error. But when I run the same system with 4, 2 or 1 processor, the symulation goes fine. I´ve already tried to enhance the

[gmx-users] How to use different reference structures for g_covar and g_anaeig

Dear All, I have two specific questions: 1.I have been to do COMBINED ESSENTIAL dynamics by concatenating two trajectories. I calcualted the covariance matrix using the default options of g_covar. This should presumably use the average structure for fitting. Now I want to use one of a different

Re: [gmx-users] SGI Altix stack traceback

Aline Rossi wrote: Hi All, the 3.3.1 version of gromacs was installed on A SGI Altix 3700 BX2. When I run mdrun_mpi_f using 8 processors for a ~500k atoms system, i receive the follwing error. But when I run the same system with 4, 2 or 1 processor, the symulation goes fine. I´ve already

Re: [gmx-users] How to use different reference structures for g_covar and g_anaeig

[EMAIL PROTECTED] wrote: Dear All, I have two specific questions: 1.I have been to do COMBINED ESSENTIAL dynamics by concatenating two trajectories. I calcualted the covariance matrix using the default options of g_covar. This should presumably use the average structure for fitting. Now I want

[gmx-users] NOC 3.0 is released

New version NOC-3.0 is released for Windows/Linux/Mac OSX/FreeBSD/Solaris with source code. Downloading is available at http://noch.sourceforge.net NOC is: a easy and fast protein explorer for structure visulization, analysis a powerful tool for crystallographic mapping, modeling and

RE: [gmx-users] compatibility of MOPAC charges with GROMACS ?

To get more rigorously derived figures, and to calculate charges, I thought of using MOPAC http://www.openmopac.net/index.html I imagine that the bond lengths and angles from MOPAC will be reliable. My question is really how compatible the charges are with the GROMACS topologies? Would

Re: [gmx-users] SGI Altix stack traceback

Aline Rossi wrote: Hi All, the 3.3.1 version of gromacs was installed on A SGI Altix 3700 BX2. When I run mdrun_mpi_f using 8 processors for a ~500k atoms system, i receive the follwing error. But when I run the same system with 4, 2 or 1 processor, Well gromacs 3.3.1 certainly works on

[gmx-users] water only

Hi, I want to create a input file of pure water other than the default one, but I don't know how to get started. Any suggestion is helpful and appreciated! LQ ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] gromacs future development guidelines?

Hi Al.. Well, first of all sorry if this message becomes a bit out of the scope of the list. Since I've heard a lot of time ago somewhere in here that the gromacs 4.0was in development, today I remembered that and decided to ask google to give this a try. I basically found this 2 documents

Re: [gmx-users] water only

Liqun He wrote: Hi, I want to create a input file of pure water other than the default one, but I don't know how to get started. Any suggestion is helpful and appreciated! Read chapter five thoroughly, and/or ask a more specific question. Mark

Re: [gmx-users] compatibility of MOPAC charges with GROMACS ?

So what you really need to do, once you have worked out which forcfield you are going to use, go back to the documentation / papers for that particular forcefield, see how they generated the parameters, then use that same procedure for the new parameters / molecules you want to generated.

Re: [gmx-users] How to use different reference structures for g_covar and g_anaeig

Hi Shridhar, g_covar does not use the average structure for fitting. It uses the structure supplied with -s for fitting and from the fitted trajectory calculates the average structure to determine the deviations from. First calculating the average structure and use that for fitting is