Hi there, I am using gromacs-4.6.1 with this mdp file:
integrator = md ; leap-frog integrator nsteps = 3000000 ; 6.0 ns dt = 0.002 ; 2 fs nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 5 ps nstcalcenergy = 100 ; nstxtcout = 5000 ; xtc every 10 ps xtc_precision = 100 continuation = yes ; Restarting 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 ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 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) nstcalclr = 10 cutoff-scheme = Group vdwtype = Cut-off vdw-modifier = Potential-shift coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT coulomb-modifier = Potential-shift tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K energygrps = complex Water ; group(s) to write to energy file pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com pbc = xyz ; 3-D PBC DispCorr = EnerPres ; account for cut-off vdW scheme gen_vel = no ; Velocity generation is off gen-seed = 128742 ; number of steps for center of mass motion removal nstcomm = 1000 the mdout.mdp file says nstcalclr = 10, but gmxdump of the tpr file says nstcalclr = 0. If I set rvdw = 1.4 (> rlist), gmxdump of the file tpr is now correct to nstcalclr = 10. I have double checked the manual but I couldn't find the reason of this behaviour. is this a bug or am I doing wrong somewhere?? thanks for any helps and Andrea Spitaleri PhD D3 - Drug Discovery & Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 -- 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
