[gmx-users] Questions about free energy calculation tutorial

[Justin Lemkul]

On 10/27/16 11:35 AM, gozde ergin wrote:
> Dear all,
>
> I follow the Justin’s free energy calculations: Methane in Water tutorial. (Thanks Justin!)
> I would like to ask two questions:
>
> 1) Is there specific reason to use sd integrator?

Langevin dynamics gives better sampling.

> 2) Methane molecules is free to sample every x,y,z point in the water bulk.
>     I would like to apply a flat-bottom restraint and keep methane molecule in the centre of bulk.
>     I want to prevent methane movement in z direction.
>     Do you have any idea how to remove the effect of flat-bottom restraint afterwards?
>

You're confining it to a spherical volume, so you need to account for that 
entropic contribution.

-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

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