Hi, How large is your perturbed region and your normal region? The FEP short-ranged kernels run on the CPU, and are not written very well for performance. So the larger the perturbed region, the worse things get. Because there's a lot of extra CPU work when running FEP, you may see improvements from also adding -pme gpu -bonded gpu to your mdrun invocation, by moving such work off the CPU.
BTW lincs-order=12 is uselessly large, but is not the problem here. Mark On Fri, 15 Mar 2019 at 06:16 praveen kumar <praveen...@gmail.com> wrote: > 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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