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

Harry Mark Greenblatt harry.greenblatt at weizmann.ac.il
Thu Dec 4 10:17:24 CET 2014


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

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.

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)?




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


Harry.Greenblatt at weizmann.ac.il<mailto:Harry.Greenblatt at weizmann.ac.il>

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