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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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