I am trying to run a temperature equilibration of my system and I get the following error:
======================= NOTE 1 [file nvt.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file nvt.mdp]: Center of mass removal not necessary for Andersen. All velocities of coupled groups are rerandomized periodically, so flying ice cube errors will not occur. ERROR 1 [file nvt.mdp]: nstcomm must be 1, not 100 for Andersen, as velocities of atoms in coupled groups are randomized every time step ======================= but I don't even have in my nvt.mdp any values for the nstcomm or restriction of center of masses translations or rotation. So I honestly do not know what is happening here. Do anybody have an idea of what is going on? This are the parameters for my cvt.mdp: ====================================================== define = -DPOSRES ; position restrain for waters ; Run parameters integrator = md-vv ; velocity Verlet algorithm nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 1 fs, largely irrelevant with Verlet rcoulomb = 333.3 ; short-range electrostatic cutoff (in nm) rvdw = 333.3 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = cutoff ; cutoff treatment ; Temperature coupling is on tcoupl = andersen ; Andersen thermostat tc-grps = System ; couple system to bath tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K nstcomm = 1 ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ===================================================================== Kindly, Lazaro -- 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.
