On 14/06/2012 4:39 PM, James Starlight wrote:
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
You've asked about this before...
http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html
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 .
Have you followed g_membed -h and their published method? You've not
shown your command lines, so it's impossible for anyone to know what
you're doing.
Mark
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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