This input has no information about implicit solvent and a simple google
search immediately yields mdp examples using gbsa. As far as performance
is concerned, we don't know the specs of your machine or the size of
your system. With cutoff electrostatics and a cutoff of 5 nm, one can
expect quite a bit of scaling with system size beyond linear.
Alex
On 6/24/2018 1:04 AM, Chhaya Singh wrote:
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.
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