Just do it! ;-) mdrun -nsteps 1
Mark On Fri, Sep 19, 2014 at 9:29 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > I mean is the "last frame ... time", the time for the frame of the cpt > file, or the frame right before the frame of the cpt file? > > On Fri, Sep 19, 2014 at 3:28 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > > > I ran gmxcheck on an old cpt file: > > > > Command line: > > gmxcheck -f nve1.cpt > > > > Checking file nve1.cpt > > Precision mismatch for state entry box, code precision is float, file > > precision is double > > Precision mismatch for state entry x, code precision is float, file > > precision is double > > Precision mismatch for state entry v, code precision is float, file > > precision is double > > > > # Atoms 30360 > > Last frame -1 time 838.960 > > > > > > Item #frames Timestep (ps) > > Step 1 > > Time 1 > > Lambda 1 > > Coords 1 > > Velocities 1 > > Forces 0 > > Box 1 > > > > > > So, if a check point file is written at frame 1, and the first frame of > > the whole simulation is frame 0, gmxcheck of the checkpoint file should > > give last frame ... time 000.000 ? or 000.002, suppose the time step is 2 > > fs? > > > > > > > > On Fri, Sep 19, 2014 at 1:43 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > >> On Fri, Sep 19, 2014 at 7:23 PM, Johnny Lu <johnny.lu...@gmail.com> > >> wrote: > >> > >> > Sorry for not being clear about the question. > >> > > >> > 1. If I start with NVT with thermostat A, and then continue with NPT > >> with > >> > thermostat A, and barostat B, will the internal variables of > thermostat > >> A > >> > stays the same, upon transitioning from the NVT ensemble to NPT > >> ensemble? > >> > 2. If I start with a NPT ensemble with thermostat A and barostat B > with > >> > timestep 1 fs, and then continue with a NPT ensemble with thermostat > A, > >> > barostat B, and timestep 0.5 fs, will the internal varaibles of > >> thermostat > >> > A and barostat B stays the same? > >> > > >> > >> Probably, but you can play with grompp with various combinations of -f > >> files and whether you give a checkpoint with -t and you can observe the > >> differences in the resulting .tpr files with gmx check -s1 -s2. > >> > >> Mark > >> > >> > >> > Yes, the -cpnum will help a lot. Guess I will try that in next phase > of > >> the > >> > simulation. Thanks. > >> > > >> > On Fri, Sep 19, 2014 at 1:04 PM, Mark Abraham < > mark.j.abra...@gmail.com > >> > > >> > wrote: > >> > > >> > > On Fri, Sep 19, 2014 at 6:39 PM, Johnny Lu <johnny.lu...@gmail.com> > >> > wrote: > >> > > > >> > > > Hi. > >> > > > > >> > > > If I change ensemble (say, from NVT to NPT) but use the same > >> > > > thermostat/barostat, will the internal variables of the > >> > > thermostat/barostat > >> > > > stays the same (like how many step later to couple the system to > >> > > > thermostat)? > >> > > > > >> > > > >> > > I don't know what you're asking. nstpcouple and nsttcouple act > >> > > independently, though in practice there are restrictions. > >> > > > >> > > If I want to continue from a particular saved frame of the > simulation > >> > > > (saved x,v,F, energy but not cpt file), and change the ensemble, > is > >> > > grompp > >> > > > <http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp> > the > >> > only > >> > > > way to go? > >> > > > >> > > > >> > > If you haven't got a checkpoint for that time, then grompp is your > >> only > >> > > friend for starting there. > >> > > > >> > > Can I make grompp to number the cpt files that it saves (like > >> > > > part0001.cpt, part0002.cpt...) ? > >> > > > > >> > > > >> > > grompp doesn't write checkpoint files. Do you want mdrun -cpnum? > >> > > > >> > > Mark > >> > > > >> > > > >> > > > Sorry for being nitpicky. > >> > > > > >> > > > Thanks again. > >> > > > -- > >> > > > 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. > -- 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.