Your EM is unrelated to dynamics. I mean, it could, but we don't know
anything about your simulated system. I am of course assuming that your
MPI setup is optimal for gmx and you actually get to use those 16
threads, assuming those aren't an emulation of some sort.
On 6/24/2018 1:33 AM, Chhaya Singh wrote:
Hi,
I have attached the energy minimization mdp file.
please look through it .
cpp =
/lib/cpp ; prepocessor of
the current machine
define =
-DFLEXIBLE ; -DPOSRES,
-DPOSRES_IONS ;DFLEX_SPC; FLEXible SPC and POSition REStraints
integrator =
steep ; steepest descent
algorithm
dt =
0.005 ; time step in ps
nsteps =
5000 ; number of steps
emtol =
100 ; convergence
criterion
emstep =
0.05 ; intial step size
constraints = none
constraint-algorithm = lincs
unconstrained-start =
no ; Do not constrain
the start configuration
;shake_tol = 0.0001
nstlist =
0 ; step frequency
for updating neighbour list
ns_type =
simple ; grid ; method
for nighbour searching (?)
nstxout =
100 ; frequency for
writing coords to output
nstvout =
100 ; frequency for
writing velocities to output
nstfout = 0 ; frequency for writing forces to output
nstlog = 100 ; frequency for writing energies to log file
nstenergy = 100 ; frequency for writing energies to energy file
nstxtcout = 0 ; frequency for writing coords to xtc traj
xtc_grps = system ; group(s) whose coords are to be written in
xtc traj
energygrps = system ; group(s) whose energy is to be written in
energy file
pbc = no ; use pbc
rlist = 1.4 ; cutoff (nm)
coulombtype = cutoff ; truncation for minimisation, with large
cutoff
rcoulomb = 1.4
vdwtype = cut-off ; truncation for minimisation, with large
cutoff
rvdw = 1.4
nstcomm = 0 ; number of steps for centre of mass motion
removal (in vacuo only!)
Tcoupl = no
Pcoupl = no
"min-implicit.mdp" 40L,
2616C
1,1 Top
the system I am using has the following information:
PBS -l select=1:ncpus=16:mpiprocs=16
#PBS -l walltime=24:00:00
On 24 June 2018 at 13:00, Alex <nedoma...@gmail.com> wrote:
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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