Dear Gromacs Users! I've forced with the problem durin insertion of my protein into pre-equilibrated bilayer via G_Membed.
I've done all steps in accordance to the KALP tutorial ( I've oriented both membrane as well as the protein in the same dimensions merged both topologies and gro files in the merged.gro file ) but after processed via grompp I've recieved warning WARNING 1 [file gmembed.mdp]: Can not exclude the lattice Coulomb energy between energy groups if I scip this message by maxwarn oprtins, g_membed remove only 10 lipids ( while > 40 are overlapped with the protein ) and during further g_membed's md_run I've obtained lincs warning and my system is crushed . I'm using berger lipids and that mdp file for the G_membed integrator = md energygrps = Protein freezegrps = Protein freezedim = Y Y Y energygrp_table energygrp_excl = Protein Protein emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Bond parameters 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 cels 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) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT pbc = xyz ; 3-D PBC Could you tell me where is the problem in my case might be? James
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