Hi Mark,
So basically, in order to reproduce the simulation, I need to fix both seed numbers in the .mdp file right ...?? However, I can find the ld-seed number from the .log file but I didn't find any gen-seed number. So in which file I could get the gen-seed number if the previous simulation was done considering gen-seed=-1....?? Another question is that, Is ld-seed number is also taking random velocity from Boltzmann distribution...? So, if gen-seeds are same but ld-seeds are different, can I call it as a different simulation for the same starting structure...? Thanks. Sayan -- Sayan Maity Workgroup of Prof. Dr. Ulrich Kleinekathöfer Ph.D. Student/Research Associate Jacobs University Bremen gGmbH, Germany https://www.jacobs-university.de/directory/maity ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abra...@gmail.com> Sent: Thursday, January 24, 2019 9:20:41 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Doubts regarding gen-seed, ld-seed and .cpt file. Hi, Both these seeds are fixed after you run grompp. That has no relationship to whether velocities are present from any input file. There is also no difference between NVT and NPT. I assume that your non-reproducible cases are each running grompp with one of these seed values set to -1, in which case grompp can picks a different value each time you run it. Otherwise, please show your command lines :-) Mark On Wed, 23 Jan 2019 at 16:55 Maity, Sayan <s.ma...@jacobs-university.de> wrote: > Dear All, > > > I have a doubt regarding the ld-seed no and .cpt file. If you repeat a > simulation with the same .cpt file but different ld-seed no, my guess I > should get the same trajectory running in the serial node (1node+1core ), > as because of all the velocities are stored in the .cpt file. I did this > test but the trajectories are different unless I fixed the ld-seed no. So, > my point is what is the significance of using .cpt file when you are doing > a production run from an equilibration as velocity is already there in the > .gro file....?? and why ld-seed no is controlling the dynamics not the > gen-seed....? I checked that for nvt I need to specify both gen-seed and > ld-seed in order to reproduce the trajectory, but from npt, I only need the > ld-seed to reproduce the trajectory. Could you please clarify my doubts...?? > > > Thanks. > > > Regards, > > Sayan > > -- > > Sayan Maity > > Workgroup of Prof. Dr. Ulrich Kleinekathöfer > > Ph.D. Student/Research Associate > > Jacobs University Bremen gGmbH, Germany > > > https://www.jacobs-university.de/directory/maity > -- > 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/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.
