Re: [gmx-users] Check point file
Note the .cpt file is a snap shot file, like a .gro coordinate file. It saves the state of the system at a particular point of time in a manner that you can have an exact restart at that time. You can still continue from 80ns relatively closely using the appropriate files you already have, you are not starting a "brand new" simulation. You can also join together the trajectory and energy files once it is completed. gmx grompp -f 400Kfor20ns.mdp -p topol.top -c 80ns.gro -e 0-80ns.edr -o continuation.tpr gmx mdrun -s continuation.tpr Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 25 Jun 2019 at 01:08, Alex wrote: > > Hi Mark > Actually the simulation I am talking about is an annealing simulation in > which the system are being annealed from room temperature to 400 k during a > 80 ns simulation and then the temperature are being ramped down again to be > at room temperature at 100 ns. Now I just want to keep continuing the > annealing from 80 ns (keeping the temperature at 400 k) instead of ramping > down. And If I start a completely brand new simulation the way you > mentioned, it does not continue the simulation at the annealed temperature > of my previous simulation. > I wish the state.cpt was also truncate-able likes the xtc and trr files to > have all at 80 ns. > > Regards, > Alex > > On Mon, Jun 24, 2019 at 5:41 AM Mark Abraham > wrote: > > > Hi, > > > > On Mon., 24 Jun. 2019, 11:21 Alex, wrote: > > > > > Thanks Mark. > > > With not be able to append to the simulation files, you mean, I should > > not > > > use the "-cpi state.cpt" in the gmx mdrun, right? > > > > > > No, I mean you can't use -append. You have no relevant file for -cpi. > > > > > If > > > > > so, then, the > > > simulation is a completely brand new simulation excepts that it use -c > > > case.80ns.gro file as starting frame from t = 0.0. Then does the > > > trjcat/eneconv used for later concatenation know that the new outputs > > > should be assigned to the time t = 8000*1*? > > > > > > > The link I gave earlier has hints for how to prepare for this to go > > smoothly. > > > > In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything > > > are being continued from t = 10. > > > > > > > Yes > > > > Mark > > > > > > > Thank you. > > > Alex > > > > > > On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham > > > wrote: > > > > > > > Hi, > > > > > > > > No, that isn't meaningful. Follow > > > > > > > > > > > > > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart > > > > but > > > > for the -c option, pass a file containing the desired frame extracted > > > from > > > > your .trr file. You will not be able to append to the simulation files, > > > but > > > > once the simulation is complete, you can concatenate all the files with > > > > trjcat/eneconv. > > > > > > > > Mark > > > > > > > > On Sun, 23 Jun 2019 at 22:53, Alex wrote: > > > > > > > > > Dear all, > > > > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > > > > > case.100ns.cpt ... all are here, I want to truncate the xtc file at > > 80 > > > > ns > > > > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr > > file. > > > > > Everything is clear for me except the case.cpt file for which is not > > > > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > > > > > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > > > > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > > > > > > > > > Thank you. > > > > > Alex > > > > > -- > > > > > 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/Sup
Re: [gmx-users] Check point file
Hi Mark Actually the simulation I am talking about is an annealing simulation in which the system are being annealed from room temperature to 400 k during a 80 ns simulation and then the temperature are being ramped down again to be at room temperature at 100 ns. Now I just want to keep continuing the annealing from 80 ns (keeping the temperature at 400 k) instead of ramping down. And If I start a completely brand new simulation the way you mentioned, it does not continue the simulation at the annealed temperature of my previous simulation. I wish the state.cpt was also truncate-able likes the xtc and trr files to have all at 80 ns. Regards, Alex On Mon, Jun 24, 2019 at 5:41 AM Mark Abraham wrote: > Hi, > > On Mon., 24 Jun. 2019, 11:21 Alex, wrote: > > > Thanks Mark. > > With not be able to append to the simulation files, you mean, I should > not > > use the "-cpi state.cpt" in the gmx mdrun, right? > > > No, I mean you can't use -append. You have no relevant file for -cpi. > > > If > > > so, then, the > > simulation is a completely brand new simulation excepts that it use -c > > case.80ns.gro file as starting frame from t = 0.0. Then does the > > trjcat/eneconv used for later concatenation know that the new outputs > > should be assigned to the time t = 8000*1*? > > > > The link I gave earlier has hints for how to prepare for this to go > smoothly. > > In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything > > are being continued from t = 10. > > > > Yes > > Mark > > > > Thank you. > > Alex > > > > On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham > > wrote: > > > > > Hi, > > > > > > No, that isn't meaningful. Follow > > > > > > > > > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart > > > but > > > for the -c option, pass a file containing the desired frame extracted > > from > > > your .trr file. You will not be able to append to the simulation files, > > but > > > once the simulation is complete, you can concatenate all the files with > > > trjcat/eneconv. > > > > > > Mark > > > > > > On Sun, 23 Jun 2019 at 22:53, Alex wrote: > > > > > > > Dear all, > > > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > > > > case.100ns.cpt ... all are here, I want to truncate the xtc file at > 80 > > > ns > > > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr > file. > > > > Everything is clear for me except the case.cpt file for which is not > > > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > > > > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > > > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > > > > > > > Thank you. > > > > Alex > > > > -- > > > > 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. > -- 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] Check point file
Hi, On Mon., 24 Jun. 2019, 11:21 Alex, wrote: > Thanks Mark. > With not be able to append to the simulation files, you mean, I should not > use the "-cpi state.cpt" in the gmx mdrun, right? No, I mean you can't use -append. You have no relevant file for -cpi. > If > so, then, the > simulation is a completely brand new simulation excepts that it use -c > case.80ns.gro file as starting frame from t = 0.0. Then does the > trjcat/eneconv used for later concatenation know that the new outputs > should be assigned to the time t = 8000*1*? > The link I gave earlier has hints for how to prepare for this to go smoothly. In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything > are being continued from t = 10. > Yes Mark > Thank you. > Alex > > On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham > wrote: > > > Hi, > > > > No, that isn't meaningful. Follow > > > > > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart > > but > > for the -c option, pass a file containing the desired frame extracted > from > > your .trr file. You will not be able to append to the simulation files, > but > > once the simulation is complete, you can concatenate all the files with > > trjcat/eneconv. > > > > Mark > > > > On Sun, 23 Jun 2019 at 22:53, Alex wrote: > > > > > Dear all, > > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > > > case.100ns.cpt ... all are here, I want to truncate the xtc file at 80 > > ns > > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr file. > > > Everything is clear for me except the case.cpt file for which is not > > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > > > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > > > > > Thank you. > > > Alex > > > -- > > > 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] Check point file
Thanks Mark. With not be able to append to the simulation files, you mean, I should not use the "-cpi state.cpt" in the gmx mdrun, right? If so, then, the simulation is a completely brand new simulation excepts that it use -c case.80ns.gro file as starting frame from t = 0.0. Then does the trjcat/eneconv used for later concatenation know that the new outputs should be assigned to the time t = 8000*1*? In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything are being continued from t = 10. Thank you. Alex On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham wrote: > Hi, > > No, that isn't meaningful. Follow > > http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart > but > for the -c option, pass a file containing the desired frame extracted from > your .trr file. You will not be able to append to the simulation files, but > once the simulation is complete, you can concatenate all the files with > trjcat/eneconv. > > Mark > > On Sun, 23 Jun 2019 at 22:53, Alex wrote: > > > Dear all, > > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > > case.100ns.cpt ... all are here, I want to truncate the xtc file at 80 > ns > > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr file. > > Everything is clear for me except the case.cpt file for which is not > > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > > > Thank you. > > Alex > > -- > > 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] Check point file
Hi, No, that isn't meaningful. Follow http://manual.gromacs.org/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart but for the -c option, pass a file containing the desired frame extracted from your .trr file. You will not be able to append to the simulation files, but once the simulation is complete, you can concatenate all the files with trjcat/eneconv. Mark On Sun, 23 Jun 2019 at 22:53, Alex wrote: > Dear all, > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > case.100ns.cpt ... all are here, I want to truncate the xtc file at 80 ns > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr file. > Everything is clear for me except the case.cpt file for which is not > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > Thank you. > Alex > -- > 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] Check point file
Check point files are generated as the simulation runs, and it keeps the last and 2nd last one generated. They are used to continue a simulation if the system crashes, or even extend an existing system. You won't have a copy of the check point file from 80ns. The best you can do is supply the coordinate file (.gro), trajectory file (.trr), and energy file (.edr) from the 80ns time, and extend the simulation time from those files. Whether that is suitable for your purposes, i.e. accurate enough etc, that is for you to decided. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 24 Jun 2019 at 06:53, Alex wrote: > > Dear all, > I have a 100 ns simulation, the case.100ns.xtc, case.100ns.trr, > case.100ns.cpt ... all are here, I want to truncate the xtc file at 80 ns > (case.80ns.xtc, case.80ns.trr) and continue it by using a new tpr file. > Everything is clear for me except the case.cpt file for which is not > possible to have the case.80ns.cpt unlike the case.80ns.xtc and trr. > So, I wonder if it is meaningful if I use the case.100ns.cpt,, > case.80ns.xtc and case.80ns.trr to continue from 80 ns point? > > Thank you. > Alex > -- > 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] check point file
Hi, Please try a quick google search first ;-) Mark On Fri, May 29, 2015 at 6:06 PM Atila Petrosian wrote: > Dear gromacs users > > I have a general question about cpt file. > > Is cpt file created every time mdrun is used, automatically? Or should I > use an special option to create a cpt file? > > For example, if the power fails, how to use the cpt file to resume mdrun? > > Any help will highly appreciated. > -- > 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.
