[gmx-users] Output Files

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 6 20:23:55 CEST 2006

Justin M. Shorb wrote:
> Hello users,
> I am fairly confident that I know the answer to this question, but for a 
> minor plea, I decided I would ask it here anyway. From the manual and 
> the online archives, it appears that you can only save forces to a trr 
> file (not xtc). Also, you can only choose to output specific groups to 
> xtc (not possible with trr). What I would like to do is save the forces 
> on a specific group nearly every timestep, but keep all the atoms only 
> for rough observation of the system (larger number of steps between 
> output). My guess is that I want the saving of groups that is allowed 
> with xtc, but with the precision and forces that is allowed with trr. 
> And therefore I am stuck between a rock and a hard place.
> Please correct me if I'm wrong, otherwise I think I'll have to re-write 
> the output code. (If I need to rewrite it, any suggestions in the regard 
> would also be welcome.) Thanks in advance!

I'm afraid you're correct. It would even be useful to sum up forces, say 
the total force on a group of atoms, and just output that. It is not 
implemented though. If you embark on coding, you can use the "User 
groups" that are in the mdp file already. They are not used in any other 
part of the code.

> Justin
> _________________________________________________________________
> Justin M. Shorb            Phone: (608) 262-0483
> Skinner Group                shorb at wisc.edu
> University of Wisconsin-Madison,  Department of Chemistry
> 1101 University Ave., Madison, WI, 53706
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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