Re: [gmx-users] Comparing amplitudes of motions in two MD simulations

rmsf is what you are looking for. g_rmsf should help. On Jul 14, 2012, at 16:23, Igor Druz wrote: > Hello, > > I would like to compare amplitude of motion of a specific atom in two > sets of MD simulations. Something like rms of displacements about the > equilibrium position would do. In yo

[gmx-users] Re: Conceptual question: Why are MD production simulations usually run in the NVT ensemble?

Hi Justin, Thanks so much for your time. You make a very good point about NPT. My field (although I am only a second-year graduate student) is physical chemistry, and I am ignorant, unfortunately, of biochemical literature. In physical chemistry, it seems that people almost always use NVT f

Re: [gmx-users] Conceptual question: Why are MD production simulations usually run in the NVT ensemble?

On 7/14/12 11:06 AM, Andrew DeYoung wrote: Hi, I'm not sure if this is an appropriate question for the Gromacs users' mailing list. If it isn't, please forgive me and disregard this message. I asked this question on Physics Stack Exchange: Why is the canonical (NVT) ensemble often used for m

[gmx-users] Re: Comparing amplitudes of motions in two MD simulations

Igor, I think that the utilities g_rms and g_msd may be helpful with this. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at htt

[gmx-users] Conceptual question: Why are MD production simulations usually run in the NVT ensemble?

Hi, I'm not sure if this is an appropriate question for the Gromacs users' mailing list. If it isn't, please forgive me and disregard this message. I asked this question on Physics Stack Exchange: Why is the canonical (NVT) ensemble often used for molecular dynamics (MD) simulations? My questio

[gmx-users] Comparing amplitudes of motions in two MD simulations

Hello, I would like to compare amplitude of motion of a specific atom in two sets of MD simulations. Something like rms of displacements about the equilibrium position would do. In your experience, which gromacs analysis tools would be suitable for this? Any other insight into how this can be done

[gmx-users] thanks

Dear Justin, Thank you very much from your response. Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searc

Re: [gmx-users] (no subject)

On 7/14/12 3:34 AM, sara elham wrote: Dear Gromacs users I want to find the solution for my problem from mailing list, but it give me this massage: "Timeout expired. The timeout period elapsed prior to completion of the operation or the server is not responding." The website experiences inte

Re: [gmx-users] Re: Melting simulations - regd

On 7/14/12 1:02 AM, rapolu sukumar wrote: Dear Justin, Thank you for your reply, here I have one more doubt, I am using 'pcoupltype= anisotropic' in my simulationa as the polymers are aniostropic, I have searched for compressibility values of system but i couldn't find is ther

[gmx-users] (no subject)

Dear Gromacs users I want to find the solution for my problem from mailing list, but it give me this massage: "Timeout expired. The timeout period elapsed prior to completion of the operation or the server is not responding." I tried to registration again, but in the section " Type the characters