Re: [gmx-users] Regarding using random seed
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 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.
Re: [gmx-users] Regarding using random seed
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 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.
Re: [gmx-users] Regarding using random seed
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 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 > 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.
Re: [gmx-users] Regarding using random seed
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 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 > > 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? 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.
Re: [gmx-users] Regarding using random seed
Right! T. On Mar 9, 2016 12:24 PM, "neha chaudhary" 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 > 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 > > > 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? 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/Mail
Re: [gmx-users] Regarding using random seed
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 wrote: > Right! > > T. > On Mar 9, 2016 12:24 PM, "neha chaudhary" > 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 > > 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 > > > > 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 > >
Re: [gmx-users] Regarding using random seed
On 3/10/16 3:21 AM, neha chaudhary wrote: 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. "Reliability" and "reproducibility" are different things. Your results are reliable if you have (1) a sound physical model, (2) application of appropriate algorithms, and (3) sufficient sampling. Running multiple simulations addresses point 3 but not the other two. Reproducibility means you get the same average behavior, so that's related to point 3, but that does not mean that everything will be exactly the same (or even that the same .tpr will necessarily generate binary identical trajectories; see the GROMACS website for discussion on this topic). -Justin 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 wrote: Right! T. On Mar 9, 2016 12:24 PM, "neha chaudhary" 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 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 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.