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

[Mark Abraham]

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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