[gmx-users] Doubt about gmx wham analysis

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

I would like to correct myself. Actually, the COM of the two groups - Protein and Ligand are about 5 nm away at the end of the pulling process. But the rear end of the ligand is just 0.6 nm away from the closest Amino acid of the Protein. Is that reasonable for the Binding affinity calculations?

Best Regards,
Bhagyesh

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Friday, June 2, 2017 4:10:21 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

On 6/1/17 6:29 PM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> Since I have the settings pull_coord1_dim = Y Y Y, I am not sure which axis the ligand is pulled. My initial simulation box size was 5 nm in each side. To care of the pulling of the ligand in any direction I made the box size 14 in each direction filled with water. The simulation runs perfectly and ending with the ligand almost 0.6 nm away from protein. But all this takes lot of computation power due to the need for rigorous sampling. Is there any way to cut the computation cost while maintaining the accuracy?
> 

0.6 nm is not very far, especially if your solute-box distance is 14 nm (which 
would be appropriate to get a full dissociation).  There's not much to do aside 
from making sure you're using an efficient box, e.g. rhombic dodecahedron.  A 
cube is inefficient.

-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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