Hi, What is the error you are getting? What is unfortunate about temperature coupling?
Have you checked out the part of the documentation, especially the supported features on GPUs part (http://www.gromacs.org/gpu#Supported_features)? -- Szilárd On Mon, Mar 7, 2011 at 3:43 PM, kala <kalabhar...@gmail.com> wrote: > Dear friends > I am trying to run a ternary complex simulation using > gromacs. so far the simulation is time taking on my dual-core maching > 36hrs/ns. Fortunately or unfortunately I have a fermi graphics card wherein > I can run the simulation quite fast. Now the unfortunate thing is the > temperature coulpling. I am new to gmx and tweeking the mdp files is out of > my head. I seek for advice for tweeking this mdp file (which i now use for > cpu calculations) for fast md using mdrun-gpu. > My system > 725 Amino acids > 2 ligand molecules > 1 co-ordinate zn Ion > > my MDP-file > > title = Protein-ligand complex NVT equilibration > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns) > dt = 0.002 ; 2 fs > ; Output control > nstxout = 0 ; suppress .trr output > nstvout = 0 ; suppress .trr output > nstenergy = 1000 ; save energies every 2 ps > nstlog = 1000 ; update log file every 2 ps > nstxtcout = 1000 ; write .xtc trajectory every 2 ps > energygrps = Protein JZ4 > ; Bond parameters > continuation = yes ; first dynamics run > constraint_algorithm = lincs ; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > rlist = 0.9 ; short-range neighborlist cutoff (in nm) > rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) > rvdw = 1.4 ; short-range van der Waals cutoff (in nm) > ; 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 = Protein_JZ4 Water_and_ions ; two coupling groups - more > accurate > tau_t = 0.1 0.1 ; time constant, in ps > ref_t = 300 300 ; reference temperature, one for > each group, in K > ; Pressure coupling is off > pcoupl = Parrinello-Rahman ; pressure coupling is on for > NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5 ; isothermal compressibility of > water, bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr = EnerPres ; account for cut-off vdW scheme > ; Velocity generation > gen_vel = yes ; assign velocities from Maxwell distribution > gen_temp = 300 ; temperature for Maxwell distribution > gen_seed = -1 ; generate a random seed > > thanks and regards > > bharath > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
