[gmx-users] How to solvate particular regions in simulation box

[Tsjerk Wassenaar]

Hi Venkat,

First, note that there are no such things as hollow ('vacuum-filled' :p)
proteins in nature. Simulating a capsid without contents is probably
non-sensical.
Besides that, you could try insane (http://cgmartini.nl/index.php/insane).
By default it excludes the inside of a protein for placement of solvent.

Cheers,

Tsjerk

On Wed, Jul 13, 2016 at 6:50 AM, Venkat Reddy <venkat4bt at gmail.com> wrote:

> Dear all,
> I am trying to simulate virus hollow capsid using gromos54a7 forcefield.
> Since the capsid is hollow, I don't want water inside the capsid. But the
> "gmx solvate" command solvates the hollow region of capsid also. So, every
> time I manually remove the water  located inside the capsid as follows.
>
> 1) I find the com of protein using gmx traj -f -s -com -ox
> 2) Using VMD, I extract out all the water molecules with in 'r' of capsid.
> 3) I proceed to energy minimization, equillibration, and final dynamics.
>
> But the above mentioned process is not always fruitful, particularly when
> the system is very big. Hence, I would like to know whether is there any
> trick to solvate only certain regions (solvate only the regions which are
> at 'r' distance from the com of protein) in the simulation box?
>
> Thanks and regards
>
> With best wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
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-- 
Tsjerk A. Wassenaar, Ph.D.