[gmx-users] problem with lipid membrane

[Justin A. Lemkul]

Parul tew wrote:
> Dear Gmx users,
> 
>  
> 
> I am working on a transmembrane protein and my system contains protein, DPPC
> 
> bilayer, water (spc) and ions. After adding ions I energy minimized the 
> system and used trjconv to remove periodicity.  In the equilibration 

It is unnecessary to manipulate the output file at this stage.  Be sure you're 
not doing anything funny to the coordinates that cause the problem described below.

> phase the lipid molecules were entering the voids in the solvent leaving 
> the protein naked. So, I used position restraint on the Z-plane and 
> restrained the phosphate head (atom 8) and one carbon atom on each tail 
> (atoms 31, 50 with a force constant of 1,000 kJ mol/−/1 nm/−/2.
> 
> -----------------------------------------------------------
> 
> ; position restraint file for DPPC
> 
>  
> 
> [ position_restraints ]
> 
> ;  i funct       fcx        fcy        fcz
> 
>    8    1       0       0       1000
> 
>   31    1       0       0       1000
> 
>   50    1       0       0       1000
> 
>  
> 
> -----------------------------------------------------------
> 
> But after running a simulated annealing for 500ps I get a distorted 
> lipid membrane where the lipids tend to pack at one end but open at the 
> other end of the box.
> 
> After this I had put position restraint on all the atoms of the lipid on 
> the z-plane and again tried the simulated annealing but it gave the same 
> result.
> 
> I am not able to understand where I am going wrong.
> 

The fact that none of the approaches is working suggests to me that either the 
topology does not #include the position restraint file or you do not have the 
proper "define" statement in your .mdp file.  A simple restraint on P8 in the 
Z-dimension should prevent distortions; I use such a technique routinely.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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