Re: [gmx-users] RESTARTING THE CALCULATION
Hi, Then maybe the file is corrupted. What does gmx check say about it? Mark On Mon, Mar 12, 2018, 17:45 Neha Gupta wrote: > Hi, > > I gave > > gmx mdrun -s md.tpr -cpi md_step17960400.cpt > > It says, Checkpoint file corrupted or truncated or you are out of disk > space? > > I have deleted files of higher MB. Why the problem persists? > > Thanks, > Neha > > On Sun, Mar 11, 2018 at 10:55 PM, Mark Abraham > wrote: > > > Hi, > > > > Exactly as you ran the original simulation, plus pass the name of the > > latest checkpoint file to -cpi. Back up your files first. > > > > Mark > > > > On Sun, Mar 11, 2018 at 6:18 PM Neha Gupta > > wrote: > > > > > Hi gromacs users, > > > > > > I wanted to do simulations fro 50 ns. > > > > > > But, due to lack of disk space, it abruptly stopped. > > > > > > > > > I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt. > > > > > > How to restart the calculation and complete it successfully? > > > > > > Thanks, > > > Neha > > > -- > > > 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. > -- 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] RESTARTING THE CALCULATION
Hi, I gave gmx mdrun -s md.tpr -cpi md_step17960400.cpt It says, Checkpoint file corrupted or truncated or you are out of disk space? I have deleted files of higher MB. Why the problem persists? Thanks, Neha On Sun, Mar 11, 2018 at 10:55 PM, Mark Abraham wrote: > Hi, > > Exactly as you ran the original simulation, plus pass the name of the > latest checkpoint file to -cpi. Back up your files first. > > Mark > > On Sun, Mar 11, 2018 at 6:18 PM Neha Gupta > wrote: > > > Hi gromacs users, > > > > I wanted to do simulations fro 50 ns. > > > > But, due to lack of disk space, it abruptly stopped. > > > > > > I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt. > > > > How to restart the calculation and complete it successfully? > > > > Thanks, > > Neha > > -- > > 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.
Re: [gmx-users] RESTARTING THE CALCULATION
Hi, Exactly as you ran the original simulation, plus pass the name of the latest checkpoint file to -cpi. Back up your files first. Mark On Sun, Mar 11, 2018 at 6:18 PM Neha Gupta wrote: > Hi gromacs users, > > I wanted to do simulations fro 50 ns. > > But, due to lack of disk space, it abruptly stopped. > > > I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt. > > How to restart the calculation and complete it successfully? > > Thanks, > Neha > -- > 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.
[gmx-users] RESTARTING THE CALCULATION
Hi gromacs users, I wanted to do simulations fro 50 ns. But, due to lack of disk space, it abruptly stopped. I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt. How to restart the calculation and complete it successfully? Thanks, Neha -- 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.