[gmx-users] Doubt about Free Energy Calculations using g_bar

[Justin Lemkul]

On 6/10/17 6:15 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> Just so we are on the same page, this means that if I don't touch the topology file and use the following mdp snippet, charges *are present* in the topology file for the ligand group and they are automatically set to zero while turning on vdW interactions (from 0 to 1) right ? Hence, there is no need to manually set charges to zero (The old style of doing the calculations), right?.
> 

Yes.  You can easily confirm this using energygrps between your transformed 
molecule and the rest of the system.  Coul-SR should be zero.

> Then the charges too, are turned off from 0 to 1? (1 state being the actual charges present in the topology file).
> 

Charges are turned *on* if they are defined as off in the A-state (lambda=0) and 
on in the B-state (lambda=1).

-Justin

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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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