Hi all, I thought I would try using the -membed option of mdrun to insert a helical dimer into a lipid bilayer. I¹ve followed the .mdp instructions on g_membed to generate my required .tpr file. Upon calling grommp I get:
ERROR 1 [file membed_NPT.mdp]: Energy group exclusions are not (yet) implemented for the Verlet scheme My input file can be seen below. If seems as though the Integrator is the issue, even though I¹ve picked the correct one. Is a place holder feature? Many thanks Anthony integrator = md energygrps = Protein freezegrps = Protein freezedim = Y Y Y energygrp_excl = Protein Protein nsteps = 5000000 ; 2 * 500000 = 1000 ps (2 ns) dt = 0.002 ; 2 fs nstxout = 10000 ; save coordinates every 0.2 ps nstvout = 10000 ; save velocities every 0.2 ps nstenergy = 10000 ; save energies every 0.2 ps nstlog = 10000 ; update log file every 0.2 ps continuation = yes ; Restarting after NVT 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 cels nstlist = 5 ; 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) coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT tcoupl = Berendsen ;Nose-Hoover ; More accurate thermostat tc-grps = Protein POPC SOL ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 310 310 310 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 pbc = xyz ; 3-D PBC DispCorr = EnerPres ; account for cut-off vdW scheme gen_vel = no ; Velocity generation is off nstcomm = 1 comm-mode = Linear comm-grps = POPC_Protein SOL refcoord_scaling = com -- 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.