[gmx-users] Insertion protein in the membrane via G_membed

[James Starlight]

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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