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.