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

[ram bio]

Dear Justin,

Thanks for the suggestion.

Best,

Ram

On Thu, Jan 27, 2011 at 6:46 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> --
> ========================================
>
> 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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