Re: [gmx-users] Erro in SMD simulation..

Thank you Justin so much... In case of this system rectangular (10x10x25) is working.. SMD is over with out any error.. Thank you.. On Wed, Apr 2, 2014 at 12:03 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5015557...@n6.nabble.com wrote: On 4/1/14, 2:18 PM, Kalyanashis wrote: Thank you

Re: [gmx-users] Reproducibility in free energy calculations.

On 4/19/14, 1:16 AM, sujithkakkat . wrote: Hello Justin, I tried the free energy calculations in your tutorial at different sets of conditions. Also I repeated a simulation at the same conditions with same parameters, thrice on the same computer on same number of processors. The results

Re: [gmx-users] Reproducibility in free energy calculations.

Mean of the three calculations is 4.35, standard error is 0.19. So this seems statistically consistent. If you want to get more consistent results, you'll need to run longer until the estimated statistical uncertainty is lower. Also, the estimated uncertainty is often an underestimate (BAR

[gmx-users] about tutorial on virtual sites

Hello Justin, I found that in the virtual sites section of your tutorial, the energy values of the system large positive . You had warned in the topology file that the choice of the partial charges used are not guaranteed to work always with OPLSAA . However, the momentum of inertial values

[gmx-users] running parallel simulations on different of cores

Dear gromacs users, I have been working on gromacs package for performing md simulations. recently i have started using cluster with 2 nodes with 64 cores each. I am eager to know whether a job run on 32 cores for few ns and later i continue the same job on 64 cores (or vice versa), will show any

[gmx-users] Specifying the number of OpenMP threads that g_hbond uses

Hi, From the web page http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x , it looks like parallelization for g_hbond (via OpenMP) was added in version 4.6.x. What is a typical command to run g_hbond in parallel? Since I mostly have experience with Gromacs 4.5.5 (which for

[gmx-users] how to fix center of mass

Dear Gromacs Users, I am simulating a polymer membrane, which has two boxes of water on both sides. Polymer membrane position is shifting a lot even though I used comm_mode = linear Is there a way to fix the center of the mass of polymer membrane? Thanks a lot for the suggestions! Thom --

[gmx-users] GCMC?

Dear Gromacs Developers Can some gromacs new version do Grand Canonical Monte Carlo (GCMC) simulations? Thanks! Thomas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] GCMC?

No On Apr 19, 2014 8:17 PM, Tom dna...@gmail.com wrote: Dear Gromacs Developers Can some gromacs new version do Grand Canonical Monte Carlo (GCMC) simulations? Thanks! Thomas -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] about tutorial on virtual sites

On 4/19/14, 11:06 AM, sujithkakkat . wrote: Hello Justin, I found that in the virtual sites section of your tutorial, the energy values of the system large positive . You had warned in the topology file that the choice of the partial charges used are not guaranteed to work always with