[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

[Victor Rosas Garcia]

As I understand it, this error is not dependent on the mdp file, but on
your system. Maybe you need to define a larger system.  Of course, you
could try decreasing rlist, but the value of rlist is usually dependent on
the force field you are using, so you risk breaking the physics if you
decrease rlist just to make the simulation work.

Hope this helps

Victor

2015-10-27 7:02 GMT-06:00 Alan <alanwilter at gmail.com>:

> Dear Mark, the simple
> em.mdp:
> integrator               = steep
> nsteps                   = 500
>
> does not work anymore with GMX 5.1.
>
>   ERROR: The cut-off length is longer than half the shortest box vector or
>   longer than the smallest box diagonal element. Increase the box size or
>   decrease rlist.
>
> How to make it work again and still keep the em.mdp the smallest, simplest
> possible?
>
> Thanks,
>
> Alan
>
> On 27 August 2014 at 17:09, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> > You only need the integrator :-) Default for everything else works.
> >
> > Mark
> > On Aug 27, 2014 4:24 PM, "Alan" <alanwilter at gmail.com> wrote:
> >
> > > Hi there,
> > >
> > > I need a very simple em.mdp and md.mdp, to simply test my generated GMX
> > > files from ACPYPE.
> > >
> > > It contains just a single small molecule without solvent. I just need
> to
> > > test if the topology file is OK (i.e. if grompp and mdrun will accept
> > it),
> > > so I used to use these parameters with GMX 4:
> > >
> > > em.mdp:
> > > cpp                      = /usr/bin/cpp
> > > define                   = -DFLEXIBLE
> > > integrator               = steep
> > > nsteps                   = 500
> > > constraints              = none
> > > emtol                    = 1000.0
> > > emstep                   = 0.01
> > > nstcomm                  = 1
> > > ns_type                  = simple
> > > nstlist                  = 0
> > > rlist                    = 0
> > > rcoulomb                 = 0
> > > rvdw                     = 0
> > > Tcoupl                   = no
> > > Pcoupl                   = no
> > > gen_vel                  = no
> > > nstxout                  = 1
> > > pbc                      = no
> > >
> > > md.mdp:
> > > cpp                      = /usr/bin/cpp
> > > define                   = ;-DFLEXIBLE
> > > integrator               = md
> > > nsteps                   = 500
> > > constraints              = none
> > > emtol                    = 1000.0
> > > emstep                   = 0.01
> > > comm_mode                = angular
> > > ns_type                  = simple
> > > nstlist                  = 0
> > > rlist                    = 0
> > > rcoulomb                 = 0
> > > rvdw                     = 0
> > > Tcoupl                   = no
> > > Pcoupl                   = no
> > > gen_vel                  = no
> > > nstxout                  = 1
> > > pbc                      = no
> > >
> > > But these parameters won’t work anymore with GMX 5. Can someone suggest
> > me
> > > the minimum alterations or completely new values so I could run a quick
> > EM
> > > and MD? And if they were compatible to both GMX 4 and 5 that’d be
> great.
> > >
> > > Many thanks in advance,
> > >
> > > Alan
> > >
> > >
> > > --
> > > Alan Wilter SOUSA da SILVA, DSc
> > > Bioinformatician, UniProt
> > > European Bioinformatics Institute (EMBL-EBI)
> > > European Molecular Biology Laboratory
> > > Wellcome Trust Genome Campus
> > > Hinxton
> > > Cambridge CB10 1SD
> > > United Kingdom
> > > Tel: +44 (0)1223 494588
> > > --
> > > Gromacs Users mailing list
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>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
> --
> Gromacs Users mailing list
>
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