Dear all, My system consists of a three chains of protein: PROA, PROB and PROCLIG (with ligand). Minimization is running properly without any error. Parameters used are: title = Minimization ; Title of run define = -DPOSRES
; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk energygrp_excl = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB SOL freezegrps = PROCLIG freezedim = Y Y Y But, while running equilibration it is giving error of the blowing up of the system like water molecule not settled, clashes etc. I ran the equilibration without adding water and also without using freeze groups. It is running perfectly. I turned off constraints and pressure coupling while using freezegroups. Parameters used: title = Protein-ligand complex NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk energygrp_excl = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB SOL freezegrps = PROCLIG freezedim = Y Y Y ; Bond parameters continuation = no ; first dynamics run constraints = none ; all bonds (even heavy atom-H bonds) constrained ; Neighborsearching ns_type = grid ; search neighboring grid cells cutoff-scheme = group nstlist = 20 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 0.9 ; 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 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 pcoupl = no ; no pressure coupling in NVT ; 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 Please guide me on this. If you have any suggestions I will really appreciate. Thanks and regards, Nirali -- 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 [email protected].
