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



-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to