[gmx-users] Understanding Force Plot in Umbrella Sampling Simulations

[Justin Lemkul]

On 11/15/14 9:48 PM, Agnivo Gosai wrote:
> Dear Users
>
> I have been following the Umbrella Sampling simulation by Dr. Lemkul and
> applying the concepts for my project.
>
> After reading Dr. Lemkul's paper associated with the tutorial , I
> understand that the Force vs Time plots will have different peaks and
> slopes , but similar profiles , in the Steered Molecular Dynamics case. It
> will vary with different pull rates and force constants. After that a
> series of sampling configurations are extracted to do the Umbrella Sampling
> simulations. Here the pull rate is 0. But this also generates Force vs Time
> plots. And through the WHAM algorithm we can find the PMF versus the pulled
> distance ( reaction coordinate ).
>
> Now I want to quantify the binding force between molecules A and B. From
> SMD I have a F vs t plot. From different samples I have different F vs t
> plots. (23 in my case ). Also I think if I take the derivative of the PMF
> with respect to the reaction coordinate , I shall have a F vs x plot.
>

Just plot the actual distances from g_dist or the pullx.xvg output.

> But I am not sure as to how to analyze the data and pin point a range for
> the "binding force " between the 2 molecules.
> Hence my questions are :- (1) Should I look at the F vs x plot generated
> from the PMF profile ?
>

What is a "binding force," exactly?

> (2) What inference should I draw from the intial F vs t plots from the SMD
> part.
>

The path along which the system evolves under the imposed bias.

> (3) What to do with the different F vs t plots from the sampling
> simulations ? The pullf and pullx are input to the WHAM algorithm but can I
> draw inferences from the individual plots ?
>

Not much.  During US, the F vs. t is just the magnitude of force applied to 
restore the restrained degree of freedom to its target value.

-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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