Hi, I am trying to run NPT equilibration on two separate systems both with ligands present in the structure.
However, I got two different errors for both of these and these are below: Fatal error: A charge group moved too far between two domain decomposition steps. Fatal error: 8 particles communicated to PME node 1 are more than 2/3 times the cut off out of the domain decomposition cell of their charge group in dimension X. My npt.mdp files looks like follows: title = NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 125000 ; 250 ps dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 5 ps nstvout = 0 ; save velocities every 5 ps nstenergy = 10 ; save energies every 5 ps nstlog = 1000 ; update log file every 5 ps ; 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 = 10 ; 50 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) rlistlong = 1.0 ; long-range neighborlist 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 = berendsen ; Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 318 318 ; reference temperature, one for each group, in K nsttcouple = 0.9999 ; 1 by default ; Pressure coupling is off pcoupl = berendsen ; Berendsen thermostat pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 1.0 ; 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 = no ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed Could you please guide me to solve the problem? -- Ankita Naithani -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
