[gmx-users] Switching Group to Verlet

[Mark Abraham]

Hi,

Do not ever do daily work as root, unless you enjoy reinstalling broken
operating systems. :-)

You've installed the MPI version. It is suffixed so everything is gmx_mpi
whatever. So you want gmx_mpi dump to inspect your tpr, but it will agree
with mdrun, of course.

You need to look at your grompp and mdrun commands to find out why what
they are doing is not what you think they are doing

Mark

On Fri, 21 Oct 2016 14:09 Mahmood Naderan <mahmood.nt at gmail.com> wrote:

> Hi,
> According to the manual, in order to edit the trp file, I have to run "gmx
> dump".
> However, there is no such file.
>
>
> root at cluster:gromacs-5.1# find . -name gmx-dump
> root at cluster:gromacs-5.1# find . -name gmxdump
> root at cluster:gromacs-5.1# find . -name gmx
> root at cluster:gromacs-5.1# ls bin/
> demux.pl             gmx-completion-gmx_mpi.bash  gmx_mpi  GMXRC.bash
> GMXRC.zsh  xplor2gmx.pl
> gmx-completion.bash  gmx-completion-mdrun.bash    GMXRC    GMXRC.csh
>  mdrun
>
> Regards,
> Mahmood
>
>
>
> On Fri, Oct 21, 2016 at 2:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Your tpr is using the group scheme. So you must be not using the .tpr you
> > intend, or not using the .mdp you intend, or grompp failed to make a tpr
> > and you didn't notice it and are using an old one. :-)
> >
> > Mark
> >
> > On Fri, Oct 21, 2016 at 12:36 PM Mahmood Naderan <mahmood.nt at gmail.com>
> > wrote:
> >
> > > Excuse me... this is a better output that shows the inconsistency
> > >
> > > mahmood at cluster:LPN$ grep -r cutoff .
> > > ./grompp.mdp:cutoff-scheme       = Verlet
> > > ./rest.mdp:cutoff-scheme       = Verlet
> > > ./md100.mdp:cutoff-scheme       = Verlet
> > > ./md.log:   cutoff-scheme                  = Group
> > > ./mdout.mdp:cutoff-scheme            = Verlet
> > >
> > >
> > > Where is the code, the scheme has been changed to Group?
> > >
> > > Regards,
> > > Mahmood
> > > --
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