Hey All, I am running a simulation of a POPC bilayer in water using a Charmm 36 forcefield. I am having trouble using cutoff-scheme=Verlet in my nvt equilibration.
My .mdp file is as follows: title = OPLS Lysozyme NVT equilibration 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 = 0 ; save coordinates every 0.2 ps nstvout = 0 ; save velocities every 0.2 ps nstenergy = 0 ; save energies every 0.2 ps nstlog = 0 ; update log file every 0.2 ps ; Bond parameters continuation = no ; 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 = 5 ; 10 fs rlist = 1.2 ; 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) rcoulomb-switch = 0 rvdw-switch = 1.0 ; long-range cut-off for switched potentials rlistlong = 1.4 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = POPC SOL ; 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 off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = No ; account for cut-off vdW scheme ; Method for doing Van der Waals vdw-type = switch ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed cutoff-scheme = Verlet *Here is the output when I run grompp to make the .tpr file:* grompp -f nvt.mdp -c em_POPC.gro -p topol.top -o nvt.tpr ERROR 1 [file nvt.mdp]: With Verlet lists only cut-off LJ interactions are supported 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. NOTE 2 [file nvt.mdp]: The switch/shift interaction settings are just for compatibility; you will get better performance from applying potential modifiers to your interactions! Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Setting gen_seed to 7358 Velocities were taken from a Maxwell distribution at 300 K Removing all charge groups because cutoff-scheme=Verlet There were 2 notes ------------------------------------------------------- Program grompp, VERSION 4.6.1 Source code file: /home/ali/Downloads/gromacs-4.6.1/src/kernel/grompp.c, line: 1593 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- -- View this message in context: http://gromacs.5086.x6.nabble.com/Charmm-36-forcefield-with-verlet-cut-off-scheme-tp5011322.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
