Hi Neha, Set
continuation = no gen_vel = yes (check http://manual.gromacs.org/online/mdp_opt.html#vel) Best, Tsjerk On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary <nehachaudhary...@gmail.com> wrote: > Thanks Tsjerk for replying, > > I want to ask one more question that to start with new velocities, what > changes I have to make and in which .mdp file? > > Best Regards, > > *Neha* > > Research Scholar, > Centre for Computational Biology and Bioinformatics, > School of Life Sciences, > Central University of Himachal Pradesh, > > > > > > On Wed, Mar 9, 2016 at 3:37 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > > > Hi Neha, > > > > You can perform a simulation first, and then extract configurations, > which > > you simulate with new starting velocities. Alternatively, you can > generate > > a number of different starting structures using elastic-network modeling, > > like with the ElNemo server. Mind to first energy minimize the resulting, > > extrapolated structures, as they may be stretchedhere and there. > > > > Hope it helps, > > > > Tsjerk > > > > On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary < > > nehachaudhary...@gmail.com> > > wrote: > > > > > Hello there, > > > > > > > > > Can anyone tell me how can I start my MD simulations with different > > > starting structure (random seed) for my protein-ligand complex. Can I > > start > > > with different sets of coordinates and velocities? If yes, how? > > > > > > > > > Thanks, > > > > > > *Neha* > > > Research Scholar, > > > Centre for Computational Biology and Bioinformatics, > > > School of Life Sciences, > > > Central University of Himachal Pradesh, > > > -- > > > 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 http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > 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 http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > 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 http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.