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

[Alan]

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