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

[Venkat Reddy]

Hi Tsjerk,
Thank you for the quick reply. I will use "insane" tool to solvate the
capsid. But my capsid has around 2 million atoms and the box dimension is
approx. 500 x 500 x 500 A3. Can "insane" handle such a huge system?

With regards
Venkat

On Wed, Jul 13, 2016 at 12:35 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote:

> 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.
> --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036