[gmx-users] Switching Group to Verlet

[Mahmood Naderan]

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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