Dear gromacs users, I wanted to do simulated annealing and I set up the .mdp file as follow...
title = OPLS 4qam MD simulation define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000000 ; 2 * 50000000 = 500000 ps (100 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 50000 ; save coordinates every 100.0 ps nstvout = 50000 ; save velocities every 100.0 ps nstenergy = 50000 ; save energies every 100.0 ps nstlog = 50000 ; update log file every 100.0 ps nstxout-compressed = 50000 ; save compressed coordinates every 100.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System ; replaces xtc-grps ; Bond parameters continuation = yes ; Restarting after NPT 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 cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme 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 Non-Protein ; 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 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 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off *;simulated annealingannealing = single periodicannealing-npoints = 4 3annealing-time = 0 4000 8000 12000 16000 20000 24000annealing-temp = 300 310 315 330 320 310 300* when I executed the mdrun with above .mdp file I got following error. *Fatal error:First time point for annealing > init_t. * Kindly tell me what could be the reason for the error. Thanks in advance *,* Surya Graduate student India. -- 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.