[gmx-users] Trajectory Problem

[David van der Spoel]

On Mon, 2005-05-16 at 10:50 -0400, Anthony Cruz wrote:
> Thank you David. But for this thime this procedure will work???
Please try and test it yourself. 
I can't see what is in your files...


> 
> On Monday 16 May 2005 10:36 am, David van der Spoel wrote:
> > 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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