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

[Mark Abraham]

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
> --
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