[gmx-users] Trajectory Problem

Anthony Cruz acb15885 at uprm.edu
Mon May 16 15:54:52 CEST 2005

Thank you David.

I have another question. I run a simulation this way:
EM in 4 CPUs. The EM.gro file I used to run PRD in 4 CPUs. Then the PRD.gro I 
used to run the MD in 4 CPUs. I want to deshuffle the result files (trr and 
gro). What will be the procedure:

1) trjconv -f MD.trr -n deshuffle_MD.ndx -o MD_des.xtc
2) trjconv -f MD_des.xtc -n deshuffle_PRD.ndx -o MD_des_PRD_des.xtc
3) trjconv -f MD_des_PRD_des.xtc -n deshuffle_EM.ndx -o final_MD_des.xtc

or only use the firs step??? and for the gro file???

On Monday 16 May 2005 7:11 am, David van der Spoel wrote:
> On Mon, 2005-05-16 at 07:02 -0400, Anthony Cruz wrote:
> > Hi:
> > I have a trr file of about 16G. When I convert the file to xtc the file
> > end in 2G. The question is if both files will have the same information
> > so I can keep only the xtc file with out any problem?
> You will loose velocities (necessary for continuation). Use gmxcheck for
> testing your files.
> > If I transform the trr (shuffle + sort) to xtc (shuffle + sort) and the
> > use the xtc (shuffle + sort) to make a des shuffle xtc the results will
> > be the same as I use the  trr (shuffle + sort)?
> Yes, although there is no obvious way to unsort a file.

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