I was doing NVT simulations on a structure constituting of 3 monomers of AGLC residue(glucose molecule) connected via 1-4 linkage. Though I have modified my nvt.mdp file for CHARMM36 but still encountering errors. The following is the nvt.mdp and I am also attaching the topology file topol.top with it.
define = -DPOSRES ; position restrain the protein ; 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 ; removing CM translation and rotation ;comm_mode = ANGULAR ;nstcomm = 1 ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching dwtype = cutoff ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 rlistlong = 1.2 rvdw-switch = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; 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 = Berendsen ; modified Berendsen thermostat tc-grps = System Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 330 330 ; reference temperature, one for each group, in K ; Pressure coupling is off 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 = 330 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed cutoff-scheme = Verlet These are the errors which I am facing NOTE 1 [file nvt.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 2905043056 Generated 85052 of the 85078 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 55198 of the 85078 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Other' turning H bonds into constraints... Setting gen_seed to 475227507 Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet WARNING 1 [file topol.top, line 699]: The bond in molecule-type Other between atoms 3 O1 and 4 A1 has an estimated oscillational period of 9.1e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Analysing residue names: There are: 3 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... ------------------------------------------------------- Program gmx, VERSION 5.0.2 Source code file: /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/readir.c, line: 3205 Fatal error: Invalid T coupling input: 3 groups, 1 ref-t values and 1 tau-t values
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