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

[Alan]

Many thanks Mark!

Alan


On 27 August 2014 18:09, 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
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