Dear Gromacs Users!<br><br>I've forced with the problem durin insertion of my protein into pre-equilibrated bilayer via G_Membed. <br><br>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<br>
<br>WARNING 1 [file gmembed.mdp]:<br> Can not exclude the lattice Coulomb energy between energy groups<br><br><br>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 .<br>
<br><br>I'm using berger lipids and that mdp file for the G_membed<br><br>integrator = md<br>energygrps = Protein<br>freezegrps = Protein<br>freezedim = Y Y Y<br>energygrp_table<br>energygrp_excl = Protein Protein<br>
<br><br><br>emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>emstep = 0.01 ; Energy step size<br>nsteps = 50000 ; Maximum number of (minimization) steps to perform<br>
<br>; Bond parameters<br>constraint_algorithm = lincs ; holonomic constraints <br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>lincs_iter = 1 ; accuracy of LINCS<br>
lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br>ns_type = grid ; search neighboring grid cels<br>nstlist = 5 ; 10 fs<br>rlist = 1.2 ; short-range neighborlist cutoff (in nm)<br>
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)<br>rvdw = 1.2 ; short-range van der Waals cutoff (in nm)<br>; Electrostatics<br>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>
pme_order = 4 ; cubic interpolation<br>fourierspacing = 0.16 ; grid spacing for FFT<br>pbc = xyz ; 3-D PBC<br><br><br>Could you tell me where is the problem in my case might be?<br>
<br><br>James<br>