Dear Gmx Users, I wish to compare simulation of peptides in water with and without excluded non-bonded parameters. My mdp file without exclusions:
; Run parameters integrator = md ; leap-frog integrator nsteps = 50000000 ; 100 ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output ; output coordinates every 25 ps nstvout = 0 ; velocities to output every 25000 steps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 5000 ; suppress (tlumic) xtc trajectory 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 cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 20 ; 10 fs vdwtype = cut-off rvdw-switch = 1.0 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) ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted potential rcoulomb ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT coulomb-modifier = Potential-shift ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein Water ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 308 308 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; pressure coupling is on for 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 ; 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 so i wish to include energygrps = Protein energygrp_excl = Protein Protein So i need to also change cutoff-scheme = group Then I get errors and notes: NOTE 1 [file md_excl.mdp]: The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators. NOTE 2 [file md_excl.mdp]: With exact cut-offs, rlist should be larger than rcoulomb and rvdw, so that there is a buffer region for particle motion between neighborsearch steps NOTE 3 [file md_excl.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb. WARNING 1 [file md_excl.mdp]: Can not exclude the lattice Coulomb energy between energy groups Istn it better for to have vdwtype = Switch/Shift in the group scheme? What are the best settings for energy exclusions in Gmx 5? Can someone provide example mdp? thanks, Steven -- 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.