[gmx-users] Making a restart file from xtc and trr ?

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 31 19:32:06 CET 2002

On Thu, 31 Jan 2002, Marc Baaden wrote:

>I have only written out velocities and forces to the trr
>and the coordinates to an xtc. Eg there are NO coordinates
>in the trr !
>I have not yet figured out whether it is possible to use the velocities
>from the trr and combine them with the corresponding coordinates
>from the xtc ?
You'll have to do some manual labour there. Without programming you would
have to use gmxdump to extract the velocities from the trajectory. I have
no idea whether trjconv will give you a pdb/g96/gro file when no
coordinates are present.

With programming, you could anyway modify trjconv to write out velocities
for a given time point. The you will have to combine in an editor with the
coords from xtc. Note however that xtc is limited precision and no perfect
continuation jobs will be possible.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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