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

[Mark Abraham]

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

Thanks
>
> Harry
>
>
>
>
>
> -------------------------------------------------------------------------
>
> Harry M. Greenblatt
>
> Associate Staff Scientist
>
> Dept of Structural Biology
>
> Weizmann Institute of Science        Phone:  972-8-934-3625
>
> 234 Herzl St.                        Facsimile:   972-8-934-4159
>
> Rehovot, 76100
>
> Israel
>
>
> Harry.Greenblatt at weizmann.ac.il<mailto:Harry.Greenblatt at weizmann.ac.il>
>
>
>
>
>
>
>
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