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

Agnivo Gosai agnivogromacs14 at gmail.com
Sun Nov 16 03:48:03 CET 2014

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.

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 ?

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

(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 ?

I am reading the WHAM paper referred in the GROMACS manual , however I
would hugely benefit from the suggestions by the forum members.

Thanks & Regard
Agnivo Gosai
Grad Student, Iowa State University.

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