Dear Francis we are running in the Xeon E5-2670 8C 2.60GHz (2 CPUs , 8 cores, 16 threads) for each temperature. and the exchange attempt frequency is 500 steps. The other system with 126 replicas run 30 ns per day ( system size of ~38000 atoms). could you please help us in solving this problem
regards singam On Monday, 24 February 2014 1:02 PM, Singam Karthick <sikar...@yahoo.in> wrote: Dear members, I am trying to run REMD simulation for poly Alanine (12 residue) system. I used remd generator to get the range of temperature with the exchange probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its drastically slow down the simulation time (for 70 pico seconds it took around 17 hours ) could anyone please tell me how to solve this issue. Following is the MDP file title = G4Ga3a4a5 production. ;define = ;-DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 12500000 ; 2 * 5000000 = 3ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 0.2 ps nstvout = 10000 ; save velocities every 0.2 ps nstxtcout = 500 ; save xtc coordinate every 0.2 ps nstenergy = 500 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy morse = no ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; 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 SOL Cl ;two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = XXXXX XXXXX XXXXX ; reference temperature, one for each group, in K ; Pressure coupling is on 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 ; 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 regards singam -- 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.
