[gmx-users] How to recenter solvent around solute

[Dimitar Pachov]

On Sat, May 7, 2011 at 11:02 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Dimitar Pachov wrote:
>
>> Hello,
>>
>> I have performed simulations of protein+ligands (solute) in truncated
>> octahedral unit cell of waters (solvent). I would like to retain the shape
>> of unit cell and have the solute centered in such a way as to be completely
>> surrounded by solvent.  At this point, I cannot achieve this although I have
>> exhausted my knowledge about using the trjconv options. My question is:
>>
>> 1. How can one recenter solvent around solute and at the same time keep
>> the original unit shape?
>>  I used the following command to get this picture:
>>
>> trjconv -f run.xtc -s run.tpr -n index-all.ndx -o traj/run-test.xtc -pbc
>> mol -center -ur compact
>>
>>
> Use -ur tric instead of -ur compact.
>


This does not work. Neither is the solute always surrounded by solvent for
every frame (it goes out of the box) nor is the original unit cell
(truncated octahedron) preserved.

I don't understand how one can achieve this, and if there is a way to do it,
why it has not been clearly explained elsewhere.

Thanks,
Dimitar




>
> -Justin
>
>
>  where for centering the solute was used and the whole system was saved to
>> the output trajectory.
>> Thanks,
>> Dimitar
>>
>>
>>
>>
> --
> ========================================
>
> 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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