[gmx-users] problem with lipid membrane

[Justin A. Lemkul]

Parul tew wrote:
> Thanks for the reply Justin,
> 
>  
> 
> This is how I added the position restraint in topology
> 
> --------------------------------------------------------------------------
> 
>  
> 
> ; Include DPPC chain topology
> 
> #include "dppc.itp"
> 
> #ifdef POSRES_LIPID
> 
> ; Position restraint for each lipid
> 
> #include "lipid_posre.itp"
> 
> #endif
> 
> --------------------------------------------------------------------------
> 
>  
> 
> And this is how the define statement is in .mdp file
> 
> --------------------------------------------------------------------------
> 
>  
> 
> title       = Simulated Annealing for B3-DPPC
> 
> define      = -DPOSRES -DPOSRES_LIPID     ; restrain protein and lipid P8
> 
> --------------------------------------------------------------------------
> 
>  
> 
> Maybe there is some problem I am not able to figure.
> 

In theory, that should work.  Please post the entirety of your .mdp file.

Have you done any prior equilibration, or have you moved straight into 
annealing?  I would suggest a restrained NVT before applying NPT or annealing 
when using the restraints.

-Justin

> Thanks.
> 
> Parul
> 
>  
> 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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