[gmx-users] Spherical Water Droplet

[Alex]

This is may be a tough one. Solvate your protein in a box of appropriate 
size, reinsert the structure in a considerably larger box, keep pbc and 
pme, no barostat (nvt). The droplet should form on its own, assuming the 
protein wets properly. You must allow for liquid-gas equilibrium, 
because part of the droplet will evaporate.

Alex

On 6/14/2017 8:44 PM, Shraddha Parate wrote:
> Dear All,
>
> I want to simulate a spherical water droplet with the protein inside it -
> without the periodic boundary conditions.
>
> I tried using pbc=no along with other parameters which have to be changed
> in the .mdp file. (as given in the documentation). Accordingly, I set the
> nstlist to 0 and ns-type to simple. I tried this step for the mdp file
> while adding ions but it generates an error regarding Ewald.
>
> Is this the right step for modifying the mdp file or should it be done in
> the later steps? Also, which other parameters has to be changed along with
> the ones specified? Is there a way to specify a radius for solvation in the
> spherical shape or hemispherical shape?
>
> Thank you in advance.
> Best regards,
> Shraddha