[gmx-users] trjconv mismatch
quyviolet at gmail.com
Wed Jan 14 10:08:01 CET 2015
Many thanks for your reply.
My command was:
trjconv_mpi -f md-*.trr -n index.ndx -timestep 100 -o md-*-timestep100.xtc
for every trr file, then concatenate by using
trjcat_mpi -f md-*-timestep100.xtc -n index.ndx -o md-timestep100.xtc
make_ndx_mpi -f md.gro -o index.ndx
and chose #1 for Protein.
Many thanks for any help!
On Wed, Jan 14, 2015 at 9:09 AM, Mark Abraham <mark.j.abraham at gmail.com>
> On Wed, Jan 14, 2015 at 9:00 AM, Jennifer Vo <quyviolet at gmail.com> wrote:
> > Dear All,
> > I have got this error while running trjconv from .xtc to .pdb file. The
> > System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is
> > the total number of Atoms in the System. The index.ndx was created from
> > md.gro file, and I Chose #1 for Protein. I don't know where is the
> > error of the mismatch here
> > Fatal error:
> > Index 135978 is larger than the number of atoms in the
> > trajectory file (36976). There is a mismatch in the contents
> > of your -f, -s and/or -n files.
> > I would appreciate for any help.
> Providing your actual command lines and interactive choices would help. If
> you'd done the right things, you'd probably not be having a problem, so
> we'll need to know what things you actually did. ;-)
> Also, use gmx check on the .xtc and .tpr files, and less on the .ndx files
> to see whether these files contain the things you think they do.
> > --
> > Gromacs Users mailing list
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users