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

[James Starlight]

I've found main reason of such crushes. It was due to the individual
internal waters wich I've included to my model as the buried to the protein
interiour ( the coordinates were copppied form X-ray structure of the same
protein).

By the way I have already performed  the same simulation with the
inclussion of the same X-ray waters but in different system with
membrane-mimicking env. consisted of Ccl4 in water. As the result there
have not been any problems with that system.

Finally I have some question about G_membed acceleration.  I've noticed
that the process of insertion of the protein in the membrane is very long
(actually it's only 50ps simulation).

During procesing of my system I've obtained notes like

NOTE 4 [file topol.top, line 19511]:
  For energy conservation with LINCS, lincs_iter should be 2 or larger.

NOTE 1 [file gmembed.mdp]:
  You are using a cut-off for VdW interactions with NVE, for good energy
  conservation use vdwtype = Shift (possibly with DispCorr)

NOTE 2 [file gmembed.mdp]:
  You are using a cut-off for electrostatics with NVE, for good energy
  conservation use coulombtype = PME-Switch or Reaction-Field-zero

The parameters for long-range and short-range interactions I've used from
my typical simulation on the lipid Gromos56-ff ( presented in the Justin's
tutorial).

Is there any other  parameters for that object wich are most suitable for
G_membed ?

James


2012/6/14 James Starlight <jmsstarlight at gmail.com>

> 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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>
>
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