[gmx-users] Placing water molecules in a defined space in the model

Justin Lemkul jalemkul at vt.edu
Wed Jan 27 02:01:58 CET 2016



On 1/26/16 7:58 PM, Agnivo Gosai wrote:
> Hello users,
>
> I am trying to prepare a topology containing an alkanethiol layer and a
> protein moelcule above it for a MD simulation using GROMACS 4.6.7.
>
> For this, I want to place the water molecules in the layer in such a way
> that they only occupy the space above the alkanethiol layer.
>
> To accomplish this , do I need to create a simulation box such that the
> layer lies on one face / side of the box (rectangular) and then use genbox
> tool ?
>
> Or there is some other method ? I have provided a link containing the
> preliminary pdb file of my system. Kindly suggest.
>

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html

-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

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