[gmx-users] mdp file for slab geometry

[anu chandra]

Dear gromacs users,

I am planing to run a membrane protein simulation with implementation of a
slab geometry, due to ion asymmetry. Below, I just copied the mdp file that
I will be using for NPT equilibration and later, for production run. Can
you please have a look and let me know if there is a need of any
modifications.

**********************************************
define                  = -DPORSE -DEQ
integrator              = md
dt                      = 0.001
nsteps                  = 25000
nstlog                  = 1000
nstxout                 = 1000
nstvout                 = 1000
nstfout                 = 1000
nstcalcenergy           = 100
nstenergy               = 1000
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
;
ewald-geometry          = 3dc              ;slab geometry
pbc                     = xyz
;
tcoupl                  = V-rescale
tc_grps                 = Protein POPC Cal_CL_SOL
tau_t                   = 0.5    0.5     0.5
ref_t                   = 305.0    305.0    305.0
;
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0     5.0
compressibility         = 4.5e-5  0      ;0 for z-direction due to vaccum
slab
ref_p                   = 1.0     1.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein_POPC Cal_CL_SOL
;
refcoord_scaling        = com

*************************************************************************

Many thanks in advance

Best regards
Anu