[gmx-users] Error while using grompp

[Sabyasachi Sahoo]

Yes, I tried using Verlet cutoff scheme but, its giving me error that
cut-off is smaller than half box vector, which implies that I am making
some error in the simulation (though I followed everything given on that
tutorial) or probably few tweaks in the .mdp or some file might help. I
will be very grateful if anyone could help in this regard.

On Fri, Sep 4, 2015 at 3:27 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> the verlet cutoff scheme seems more important for benchmarking and finding
> bottlenecks.
> I guess many people use verlet instead of group cut-off scheme now.
>
> On Thu, Sep 3, 2015 at 10:59 AM, Sabyasachi Sahoo <ssahoo.iisc at gmail.com>
> wrote:
>
> > Thanks a lot!
> >
> > On Thu, Sep 3, 2015 at 8:13 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Some of the default behaviour of GROMACS has changed since I wrote that
> > > tutorial, and I haven't updated it, sorry. You can add "cutoff-scheme =
> > > Group" to em.mdp, as a workaround
> > >
> > > Mark
> > >
> > > On Thu, Sep 3, 2015 at 4:36 PM Sabyasachi Sahoo <ssahoo.iisc at gmail.com
> >
> > > wrote:
> > >
> > > > Dear users,
> > > > I am trying to go through all the steps given in tutorial "
> > > >
> > > >
> > >
> >
> http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Topology_preparation%2c_%22What's_in_a_log_file%22%2c_basic_performance_improvements%3a_Mark_Abraham%2c_Session_1A
> > > > "
> > > > and the moment I enter the command:
> > > >
> > > > grompp -f em
> > > >
> > > > I get the following error:
> > > >
> > > > ERROR 1 [file mdout.mdp]:
> > > > With Verlet lists only full pbc or pbc=xy with walls is supported
> > > >
> > > > Has this error got something to do with the way I built my Gromacs?
> Any
> > > > help por insight to the matter is appreciated!
> > > > Thanks in advance!
> > > > --
> > > > Yours sincerely,
> > > > Saby
> > > > --
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> >
> > --
> > Yours sincerely,
> > Sabyasachi Sahoo
> > M. Tech - Computational Science
> > Supercomputer Education & Research Center
> > Indian Institute of Science - Bangalore
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-- 
Yours sincerely,
Sabyasachi Sahoo
M. Tech - Computational Science
Supercomputer Education & Research Center
Indian Institute of Science - Bangalore