thanks for the reply. How i can check the stability of integration? If i consider 2 first ns for equlibration, can I trust the rest results?
________________________________ From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Tuesday, December 11, 2012 5:01 PM Subject: Re: [gmx-users] gen-vel=no On 12/11/12 1:19 AM, Venkat Reddy wrote: > The check point file you submit will have the velocity information. > A checkpoint file is indeed a better set of information to pass to -t, but it is not clear if the OP even used -t in the invocation of grompp. If not, there will be a discontinuity in the ensemble and the initial forces are simply calculated from the potential of the initial configuration. This may or may not produce stable integration, but at the very least certainly will require some time to be discarded as new equilibration. -Justin > > On Tue, Dec 11, 2012 at 10:55 AM, Bahar Mehrpuyan > <baharmehrpu...@yahoo.com>wrote: > >> hi gmx user >> >> I've done a production simulation with gen_vel= no, but in grompp I forgot >> that use .trr file of equlibration simulation for initial velocities, >> my question is how gromacs treats with initial velocities in this case? >> >> thanks in advance. >> -- >> 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 >> > > > -- ======================================== 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
