[gmx-users] Trajectory Problem

[Anthony Cruz]

Thank you David. But for this thime this procedure will work???

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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