[gmx-users] protein movement in lipid bilayer during simulation

[Justin A. Lemkul]

ram bio wrote:
> Dear Gromacs Users,
> 
> I am performing an all-atom simulation of protein ligand complex in
> lipid bilayer , but after around 100ns, I see that the protein started
> moving in one dimension in the lipid bilayer that is it is not in the
> centre, I want the position of the protein fixed through out the
> simulation, so pl suggest regarding this..
> 

This is a normal consequence of diffusion in a periodic system.  There is no 
such thing as a "center."  For visualization purposes, just post-process your 
trajectory with trjconv.

> and is it ok if I increase the position restraints for the protein by
> changing the values of forces on x y and z dimensions in the posre.itp
> file (below) of the protein, and if so how much can i increase the
> force, so that i doesnot effect the simulation.
> 

If you're trying to get around the diffusion issue, don't.  If this is part of 
equilibration, all you're doing is setting up a higher energy barrier for the 
movement of these atoms.  The difference between 1000 and 2000 should be 
relatively minimal, as far as the end result is concerned.

-Justin

> [ position_restraints ]
> ; atom  type      fx      fy      fz
>      1     1  2000  2000  2000
>      5     1  2000  2000  2000
>      7     1  2000  2000  2000
>     10     1  2000  2000  2000
>     13     1  2000  2000  2000
>     14     1  2000  2000  2000
>     18     1  2000  2000  2000
>     19     1  2000  2000  2000
>     20     1  2000  2000  2000
>     21     1  2000  2000  2000
>     23     1  2000  2000  2000
>     26     1  2000  2000  2000
>     29     1  2000  2000  2000
>     32     1  2000  2000  2000
>     33     1  2000  2000  2000
>     34     1  2000  2000  2000
>     35     1  2000  2000  2000
>     37     1  2000  2000  2000
>     40     1  2000  2000  2000
> 
> Thanks in advance,
> 
> Ram

-- 
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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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