[gmx-users] simulation a box of water

[Justin Lemkul]

On 3/16/16 3:38 PM, Saeed Nasiri wrote:
> Thank you Justin
> I don't understand. Do I use the explicit water molecules or the model?

You're going to have to explain what this means.  Either you have water 
molecules or you don't.  If you have water molecules, you have to represent them 
using a force field.  If you want some implicit solvent, you need to delete your 
waters and use appropriate .mdp options for an implicit representation.

> and where do I used the "define = -DFLEXIBLE" option?

The .mdp file.

> please explain a bit more!
>

Make sure you've done some tutorials to have a good handle on general concepts.

-Justin

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

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

==================================================