[gmx-users] implicit solvent error

[Chhaya Singh]

Hi,

I am trying to simulate a protein in an implicit solvent in groamcs using
amber ff99sb ildn .
the mdpfile that I am using is I have shown below:


integrator          =  md
dt                  =  0.001 ;0.005    ; ps !
nsteps              =  5000000 ; total 5 ns.

nstlog                  = 5000
nstxout                 = 0  ;1000
nstvout                 = 0  ;1000
nstfout                 = 0  ;1000
nstxtcout               = 5000
nstenergy               = 5000

nstlist             =  10

cutoff-scheme       = group

rlist               =  5
rvdw                =  5
rcoulomb            =  5
coulombtype         = cut-off
vdwtype             = cut-off
bd_fric             =  0
;ld_seed             =  -1
pbc                 =  no
ns_type             =  grid  ;simple => gives domain decomposition error
constraints         = all-bonds
lincs_order         = 4
lincs_iter          = 1
lincs-warnangle     = 30

Tcoupl              = v-rescale
tau_t               = 1.0
tc-grps             = Protein
ref_t               = 310



This is the mdp file that I am using for equilibration and production run,
if there is anything that I can fix in mdp file please let me know.
I am getting very less speed using an implicit solvent in gromacs.
is there any way to increase the speed.
the speed right now I am getting is 0.47- 0.74 ns /day using one node.
please help.