On 1/6/16 2:00 PM, Nash, Anthony wrote:
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?
It's not the integrator that's the problem. It is, as the error states, the use of the Verlet cutoff scheme. Presumably "cutoff-scheme = group" would circumvent this issue.
-Justin
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
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
