Re: [gmx-users] Problem in extending simulation with state.cpt while changing number of cores
On Tue, Mar 11, 2014 at 6:17 AM, Bappa Ghosh wrote: > Thanks Mark for your reply, > > I am using gromacs version 4.6.3 with single precision. > Also I used state.cpt in mdrun , not in the tpbconv. I apologise for my > typing mistake. > Please use copy and paste when reporting problems. It's faster for you, and doesn't waste everybody's time. > So the command line was as follows- > > tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr > mdrun -s 15ns_new.tpr -o last_15ns.trr -cpi state.cpt > > It's still hard to have confidence that we are trouble shooting the right thing. Have you inspected the log file carefully for reasons and differences why mdrun did not do what you think? Note also that e.g. if there's PME tuning going on (e.g. you switched to/from GPU machine), then the Coul (SR) will not be continuous. The total potential energy should be continuous. (And Coul (SR) is a doubtful metric of anything useful, anyway) Mark > > > > On Mon, Mar 10, 2014 at 10:11 PM, Mark Abraham >wrote: > > > Please always report at least your GROMACS version! > > > > tpbconv does not take a -cpi argument, so if that is really your command > > line, then it is not doing what you think it is doing. Then mdrun has no > > option but to re-start from the only frame it knows about - the one from > > which you originally started. > > > > Mark > > > > > > On Mon, Mar 10, 2014 at 5:23 PM, Bappa Ghosh wrote: > > > > > Hello all, > > > > > > I was simulating a mixture of water and carbon-di-oxide for 20ns in one > > > node with 32 cores. After completion of 20ns run' I extended it for > > further > > > 15ns with tpbconv as follows- > > > > > > tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt > > > mdrun -s 15ns_new.tpr -o last_15ns.trr > > > > > > The last 15ns run was carried out in one node with 12 cores. > > > When I plot coulomb potential energy (short range) for whole 35ns > > > trajectory, I observe a sharp rise at the extention time (i.e at the > > > begining of last 15ns run). This sharp rise is not observed if the > number > > > of cores are kept same during extension. > > > > > > Any comments/suggestions on this observation will be beneficial to me. > > > > > > Thanks in advance. > > > > > > > > > Bappa Ghosh > > > Project Student > > > .. > > > C/O -Dr Sudip Roy > > > Scientist, > > > CSIR-National Chemical Laboratory, > > > Pune-411008,India > > > -- > > > 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] Problem in extending simulation with state.cpt while changing number of cores
Thanks Mark for your reply, I am using gromacs version 4.6.3 with single precision. Also I used state.cpt in mdrun , not in the tpbconv. I apologise for my typing mistake. So the command line was as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr mdrun -s 15ns_new.tpr -o last_15ns.trr -cpi state.cpt On Mon, Mar 10, 2014 at 10:11 PM, Mark Abraham wrote: > Please always report at least your GROMACS version! > > tpbconv does not take a -cpi argument, so if that is really your command > line, then it is not doing what you think it is doing. Then mdrun has no > option but to re-start from the only frame it knows about - the one from > which you originally started. > > Mark > > > On Mon, Mar 10, 2014 at 5:23 PM, Bappa Ghosh wrote: > > > Hello all, > > > > I was simulating a mixture of water and carbon-di-oxide for 20ns in one > > node with 32 cores. After completion of 20ns run' I extended it for > further > > 15ns with tpbconv as follows- > > > > tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt > > mdrun -s 15ns_new.tpr -o last_15ns.trr > > > > The last 15ns run was carried out in one node with 12 cores. > > When I plot coulomb potential energy (short range) for whole 35ns > > trajectory, I observe a sharp rise at the extention time (i.e at the > > begining of last 15ns run). This sharp rise is not observed if the number > > of cores are kept same during extension. > > > > Any comments/suggestions on this observation will be beneficial to me. > > > > Thanks in advance. > > > > > > Bappa Ghosh > > Project Student > > .. > > C/O -Dr Sudip Roy > > Scientist, > > CSIR-National Chemical Laboratory, > > Pune-411008,India > > -- > > 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] Problem in extending simulation with state.cpt while changing number of cores
Please always report at least your GROMACS version! tpbconv does not take a -cpi argument, so if that is really your command line, then it is not doing what you think it is doing. Then mdrun has no option but to re-start from the only frame it knows about - the one from which you originally started. Mark On Mon, Mar 10, 2014 at 5:23 PM, Bappa Ghosh wrote: > Hello all, > > I was simulating a mixture of water and carbon-di-oxide for 20ns in one > node with 32 cores. After completion of 20ns run' I extended it for further > 15ns with tpbconv as follows- > > tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt > mdrun -s 15ns_new.tpr -o last_15ns.trr > > The last 15ns run was carried out in one node with 12 cores. > When I plot coulomb potential energy (short range) for whole 35ns > trajectory, I observe a sharp rise at the extention time (i.e at the > begining of last 15ns run). This sharp rise is not observed if the number > of cores are kept same during extension. > > Any comments/suggestions on this observation will be beneficial to me. > > Thanks in advance. > > > Bappa Ghosh > Project Student > .. > C/O -Dr Sudip Roy > Scientist, > CSIR-National Chemical Laboratory, > Pune-411008,India > -- > 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] Problem in extending simulation with state.cpt while changing number of cores
Hello all, I was simulating a mixture of water and carbon-di-oxide for 20ns in one node with 32 cores. After completion of 20ns run' I extended it for further 15ns with tpbconv as follows- tpbconv -s 20ns_old.tpr -extend 15000 -o 15ns_new.tpr -cpi state.cpt mdrun -s 15ns_new.tpr -o last_15ns.trr The last 15ns run was carried out in one node with 12 cores. When I plot coulomb potential energy (short range) for whole 35ns trajectory, I observe a sharp rise at the extention time (i.e at the begining of last 15ns run). This sharp rise is not observed if the number of cores are kept same during extension. Any comments/suggestions on this observation will be beneficial to me. Thanks in advance. Bappa Ghosh Project Student .. C/O -Dr Sudip Roy Scientist, CSIR-National Chemical Laboratory, Pune-411008,India -- 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.
