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

[Pawan Kumar]

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.


> 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.

>
> 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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