[gmx-users] Doubt regarding membrane protein in POPC bilayer

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 6 14:05:17 CEST 2009

Pawan Kumar wrote:
> Respected Sir,
> Greetings from Pawan.
>     1. Were there gaps between the water and lipid headgroups?  If so,
>     the lipids may be pulling towards the solvent.  Restrain the lipids
>     and run an equilibration for a longer time.
> Gap was there when  I used a  value of 0.5 in the vdwradii.dat file. The 
> gap reduced as I decreased the value from 0.5 to 0.35 to the default of 
> 0.15. I tried all the three possibilities.
> When I used the default vdwradii.dat file and made the solvation 
> followed by simulation runs the lipids didnt pull apart. But there were 
> water molecules on the sides of the bilayer and not in the interior.

This indicates to me that the gaps are causing the problem.  Do not run 
simulations with water in or around the lipids; it is not realistic.  You can 
clean up such a starting structure, either by some clever script like those on 
the wiki, or by looking at the structure, taking note of which water molecules 
are offending, and deleting them manually from the coordinate file.

The other option is to temporarily give genbox a box that is slightly smaller in 
the x-y dimensions, so that it will try to place less water around the POPC 

>     2. 5000 steps is far too short to expect any realistic behavior for
>     lipids. Equilibration can take upwards of 10-20 ns.
> As per your suggestion I have made the final mdrun now again with 500000 
> steps. Hopefully this will work.
>     3. You haven't mentioned the contents of your .mdp file.  Maybe
>     you're doing something wrong.
> I am using the same .mdp file which I posted before. I have just removed 
> the restraints.

I don't have record of the previous email; as a general guide, post the .mdp by 
default when experiencing weird behavior.  That way the users on this list won't 
have to go combing through the archive to find it.  If you want free help, make 
it easy to help you :)


>     4. Are you using Gromos/Berger or OPLS/converted Berger for your
>     system?  There have been so many of these questions from different
>     users over the last few days that it's hard to keep track.  If you
>     are using OPLS/converted Berger you may have made a mistake in
>     translating the C6/C12 parameters.
> I am using  gromos 96 force field (G43a1) and as per your suggestion I 
> have edited the lipid.itp file to remove the part containing " 
> lipid-gromos interactions".
> Thanking you,
> Yours sincerely,
> Pawan
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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