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

[Alan]

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