[gmx-users] Trajectory Problem

[David van der Spoel]

On Mon, 2005-05-16 at 09:54 -0400, Anthony Cruz wrote:
> 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???
Please try it for a short stretch of trajectory. If you just have
protein and water shuffling doesn't do anything. 


> 
> 
> 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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-- 
David.
________________________________________________________________________
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://xray.bmc.uu.se/~spoel
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