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

[James Starlight]

Mark,

I've used commands provided in the G_membed manual

   g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000

or

   g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
-zinit 1.1 -zend 1.0 -nz 100


In both cases I've obtained the same message

There are 122 lipids in the membrane part that overlaps the protein.
The area per lipid is 0.5002 nm^2.
Maximum number of lipids that will be removed is 45.

and eventually only 10 lipids were removed. Also I've tried to do this on
another pope bilayer (consisted of bigger lipids with properly equilirated
) but I've obtained exactly the same results.


James

2012/6/14 Mark Abraham <Mark.Abraham at anu.edu.au>

>  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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