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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