[gmx-users] Spherical Water Droplet

[Justin Lemkul]

On 6/14/17 10:53 PM, Alex wrote:
> 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.
> 

Unless one applies a flat-bottom spherical potential to keep the droplet formed.

-Justin

> 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
> 

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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