Hello Sir, Thanks for your help.
I need to clear one more doubt, if I am performing MD simulations with the mentioned parameter set but using same initial structures then will it affect the reproducibility of the results. Actually, I have repeated MD simulations for my protein-ligand complex three times but I have taken the same initial structure every time using the same parameters while performing NVT simulations followed by NPT and MD run (gen-vel = no in npt.mdp and md.mdp file). Is this procedure correct if I want to testify the reliability of my results. continuation = no gen-vel = yes gen-seed = -1 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 6:36 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Right! > > T. > On Mar 9, 2016 12:24 PM, "neha chaudhary" <nehachaudhary...@gmail.com> > wrote: > > > Hi, > > > > So all I have to do is to extract different configurations from my > already > > performed MD simulation. Then I have to prepare a new system using that > > configuration with the following parameters and rerun the simulations: > > > > continuation = no > > gen_vel = yes > > gen-seed = -1 > > > > Right? > > > > > > 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 4:06 PM, Tsjerk Wassenaar <tsje...@gmail.com> > > wrote: > > > > > 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. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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