[gmx-users] Free-energy on GMX-2019.1 ( lower performance on GPU)
praveen kumar
praveenche at gmail.com
Fri Mar 15 06:16:02 CET 2019
Dear All
I am trying to run the free-energy simulation using TI method in gromacs
2019.1 in a GPU machine (containing two Nvidia Geforce 1080 TI cards ).
But unfortunately, am unable to run the free-energy simulation run on GPU.
The normal MD simulation (without free-energy )is able to run perfectly by
making use of GPU, which gives us excellent speed up in the simulation.
for example, 100 K atoms system is able to give us ~ 80 ns per day on a gpu
card. (It uses > 80 % GPU usage)
When I am trying to run the free-energy simulations for the same system,
the performance drastically falls down to ~0.02 ns per day. (It uses 0 %
GPU usage).
I am pasting the MDP files for Normal MD simulation and Free-energy
simulation below.
npt. mdp (MD simulation)
#####################################################################
title = MD simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 100000000 ; 2 * 60000000 = 200 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 100000 ; save coordinates every 10.0 ps
nstvout = 100000 ; save velocities every 10.0 ps
nstfout = 100000 ; save forces every 10.0 ps
nstenergy = 500 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every
10.0 ps, nstxout-compressed replaces nstxtcout
compressed-x-grps = System ; replaces xtc-grps
; Bond parameters
continuation = yes ; Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; H bonds constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
rvdw-switch = 1.0
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = system ; Water ; two coupling
groups - more accurate
tau_t = 0.1 ; 0.1 ; time constant, in ps
ref_t = 360 ; 340 ; reference
temperature, one for each group, in K
; Pressure coupling is on
;pcoupl =no
pcoupl = Parrinello-Rahman ; Pressure coupling on in
NPT
pcoupltype = isotropic ; uniform scaling of box
vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ;1.0 ; reference pressure, in
bar
compressibility = 4.5e-5 ; 4.5e-5 ; isothermal
compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = no ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
######################################################################
npt. mdp ( for free-energy simulation)
##########################################################################
; Run control
integrator = sd ; Langevin dynamics
tinit = 0
dt = 0.002
nsteps = 50000 ; 100 ps
nstcomm = 100
; Output control
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 500
nstenergy = 500
nstxout-compressed = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme = verlet
nstlist = 20
ns_type = grid
pbc = xyz
rlist = 1.2
; Electrostatics
coulombtype = PME
rcoulomb = 1.2
; van der Waals
vdwtype = cutoff
vdw-modifier = potential-switch
rvdw-switch = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps = system
tau_t = 1.0
ref_t = 298
; Pressure coupling is on for NPT
Pcoupl = berendsen
tau_p = 1.0
compressibility = 4.5e-05
ref_p = 1.0
; Free energy control stuff
free_energy = yes
init_lambda_state = 0
delta_lambda = 0
calc_lambda_neighbors = 1 ; only immediate neighboring windows
couple-moltype = IO ; name of moleculetype to decouple
couple-lambda0 = vdw ; only van der Waals interactions
couple-lambda1 = vdw-q ; turn off everything, in this case
only vdW
couple-intramol = no
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state 0 1 2 3 4 5 6 7 8
9 10 11 12 13 14 15 16 17 18 19 20
vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; We are not transforming any bonded or restrained interactions
bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Masses are not changing (particle identities are the same at lambda = 0
and lambda = 1)
mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Not doing simulated temperting here
temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Options for the decoupling
sc-alpha = 0.5
sc-coul = no ; linear interpolation of Coulomb (none
in this case)
sc-power = 1
sc-sigma = 0.3
nstdhdl = 10
; Do not generate velocities
gen_vel = no
; options for bonds
constraints = h-bonds ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NVT
continuation = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 12
################################################################################
for running simulation I am using the command below.:
"gmx mdrun -v -s MD.tpr -deffnm MD -nb gpu -ntomp 10 -gpu_id 0 "
Any help in solving this issue is much appreciated
Thanking you in Advance
Praveen
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