Dear Justin, Thank you for your fast reply. I found out the difference between the plots so no question about the velocity distribution.
Cheers, Nino ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Friday, November 02, 2012 5:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Pull code, Velocity distribution On 11/2/12 10:52 AM, Samadashvili Nino wrote: > Hello, > > I have been using the pull code for friction calculations. I am not > doing umbrella sampling but just pulling one slab of crystal on top of > another with the constant velocity. I would like to know how Gromacs is > calculating the pulling force (pullf.xvg) during sliding. Is the pulling > force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential? This should be correct. > I am using following parameters: > > pull = umbrella > pull_geometry = direction_periodic > pull_dim = Y Y Y > pull_start = yes > pull_ngroups = 1 > pull_group0 = ICE_A > pull_group1 = ICE_B > pull_pbcatom0 = 0 > pull_pbcatom1 = 0 > pull_vec1 = 1 0 0 > pull_rate1 = 0.004 > pull_k1 = 10000 > > Since I have pull_start=yes, does it mean that the initial spring length is > the COM distance between ICE_A and ICE_B? Yes. > Another question is regarded to the velocity distribution. I used g_traj to > plot the velocity distribution of my system which I compared with the > distribution plot calculated from the coordinates and they dont match. > The distribution calculated by Gromacs has a tail while my calculations don't > show any. Could you please tell me how is it calculated in Gromacs? How what is calculated? How are you creating your own distributions from the coordinates? -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
