[gmx-users] energy groups rerun from reduced xtc file

[Mark Abraham]

On Sun, Dec 7, 2014 at 9:54 AM, Harry Mark Greenblatt <
harry.greenblatt at weizmann.ac.il> wrote:

> BS"D
>
> Dear Mark,
>
>     Thank you for the advice; removing the checkpoint file does allow
> grompp to produce a new tpr file for mdrun.
>
> In the case, however, where the energy groups were defined before the run,
> and so it should be a simple
> case of rerunning mdrun on CPU's, the use of convert-tpr to produce a
> smaller tpr file gives the following error in
> mdrun:
>
> Software inconsistency error:
> Position restraint coordinates are missing
>
> (the DNA is restrained in these runs).
>
> So producing a new tpr file via grompp seems the only way to  go...?
>

As normal in complex software, not everything is thought about when people
add features. If you were to go back to your original grompp call and
arrange life to generate a .tpr that would have been good for mdrun without
position restraints, then you might have more luck with convert-tpr.

Mark


> Thanks
>
> Harry
>
>
>
>
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology           harry.greenblatt at weizmann.ac.il
> Weizmann Institute of Science        Phone:  972-8-934-3625
> 234 Herzl St.                        Facsimile:   972-8-934-4159
> Rehovot, 76100
> Israel
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark
> Abraham [mark.j.abraham at gmail.com]
> Sent: Thursday, December 04, 2014 1:32 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] energy groups rerun from reduced xtc file
>
> On Thu, Dec 4, 2014 at 10:16 AM, Harry Mark Greenblatt <
> harry.greenblatt at weizmann.ac.il> wrote:
>
> > BS"D
> >
> > Dear All,
> >
> >    In an attempt to save disk space while using longer simulations of a
> > DNA + Protein + solvent system,
> > I had mdrun create an xtc file with only the DNA, Protein, and ions,
> > excluding the water molecules.
> > No trr file was produced.  This is fine for many things, but since I also
> > want to look at energies between
> > defined groups, and the GPU-based calculations do not support this, I
> need
> > to to a "rerun" of the simulation with CPU's only,
> > to do the energy calculations.
> >
> > If I understood correctly, the procedure to change or introduce energy
> > groups would be:
> >
> > grompp -f yournew.mdp -c yourold.gro -t yourold.cpt -p your.top -o
> > newrerun.tpr -n yournewindexfile.ndx
> >
>
> There's no need to provide the checkpoint file. The rerun takes the
> coordinates of the old trajectory and applies the model physics in the
> .tpr. It doesn't generate new coordinates, so questions of
> trajectory/ensemble continuity do not arise. Thus, no checkpoint needed.
>
>
> > mdrun -v -s newrerun.tpr -rerun yourold.xtc -e new.edr
> >
> > The problem is that the xtc file and the initial topology no longer have
> > the same number of atoms.  I have gone through a lot of conversions,
> > to create new top and gro files without water molecules.
> >
>
> grep -v SOL does most of the work for coordinate files, and the topology
> change should be about one line in [system].
>
> Alternatively, gmx convert-tpr can make subsets of .tpr files, which should
> also be enough for your purposes.
>
> I was not, however, able to take care of cpt file, since my attempt to use
> > trjconv succeeded, but grompp does not like it because trjconv
> > does not output a cpt file.
> >
> > Is there a solution to this problem (other than having to produce
> all-atom
> > xtc or trr files)?
> >
>
> Yep, don't do work you don't need :-)
>
> Mark
>
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