Dear Gromacs users, I'm running a simulation between LASR receptor and Quercetin on Q6600, GTX 960, CPU utilization is about 90%, but GPU is only 25-30%(Nvidia X server tools).The system is only 28643 atoms and dt = 2 fs. This is the mdp settings: ; Run parametersdefine = -DPOSRES_B ; Lets seeintegrator = md ; leap-frog integratornsteps = 5000000 ; 2 * 500000 = 1000 ps (1 ns)dt = 0.002 ; 2 fs; Output controlnstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr outputnstenergy = 1000 ; save energies every 2 psnstlog = 1000 ; update log file every 2 psnstxout-compressed = 1000 ; write .xtc trajectory every 2 pscompressed-x-grps = Systemenergygrps = Protein HSL; Bond parameterscontinuation = yes ; first dynamics runconstraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrainedlincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy; Neighborsearchingcutoff-scheme = Verletns_type = grid ; search neighboring grid cellsnstlist = 10 ; 20 fsrcoulomb = 1.4rvdw = 1.4 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticspme_order = 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature coupling is ontcoupl = V-rescale ; modified Berendsen thermostattc-grps = Protein_HSL Water_and_ions ; two coupling groups - more accuratetau_t = 0.1 0.1 ; time constant, in psref_t = 300 300 ; reference temperature, one for each group, in K; Pressure coupling is offpcoupl = Parrinello-Rahman ; pressure coupling is on for NPTpcoupltype = isotropic ; uniform scaling of box vectorstau_p = 2.0 ; time constant, in psref_p = 1.0 ; reference pressure, in barcompressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correctionDispCorr = EnerPres ; account for cut-off vdW scheme; Velocity generationgen_vel = no ; assign velocities from Maxwell distributiongen_temp = 300 ; temperature for Maxwell distributiongen_seed = -1 ; generate a random seedrefcoord_scaling = com
Best regards,Hovakim Grabski -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
