[gmx-users] Lie method for binding free energy calculations

[Justin Lemkul]

On 10/25/13 11:32 AM, Sajad Ahrari wrote:
> thanks for replying. are these features available under Gromacs? and is there
> any tutorial or related material I can grasp to stand up for start?
>

My umbrella sampling tutorial covers generating a PMF.  MM/PBSA is just a 
post-processing technique, requiring software external to Gromacs.  The MD 
itself is no different and can be done with Gromacs.

-Justin

>
> On Friday, October 25, 2013 6:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/25/13 11:07 AM, Sajad Ahrari wrote:
>  > Hello dears
>  > searching through literature, many cases of LIE method application for BFE
> calculation of small molecules are on hand . but I couldn't find any report of
> using this method for interaction of small peptides and proteins. I wanted to
> know if the protocol prepared in Justin tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html)
> can be used in such case? and if so, should I apply any constrain on rotatable
> bonds of peptide along the simulation within the non-bonded state?
>
> PMF or MM/PBSA calculations are far better suited for studying these types of
> interactions.
>
>
> -Justin
>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
>
> ==================================================
>
>

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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