[gmx-users] Umbrella sampling restraining potential

[Agnivo Gosai]

Dear Users

The PMF generated by umbrella sampling of my system appears to be converged
and the calculated free energy of binding is close to that in published
literature.
I believe a necessary check for the convergence is the overlap and
smoothness of the histograms generated from sampling of the reaction
coordinate. Earlier I discussed in the forum regarding my histogram spacing
and smoothness.
Dr. Lemkul had then pointed out the rocky nature of many histograms and the
inadequate overlaps.

previous post :
http://comments.gmane.org/gmane.science.biology.gromacs.user/74659

For my system there is no experimental study and I am resorting to trial
and error. My pull force constant is 1000 kJ/mol/nm^2 whereas the only
literature doing a MD study of my system ( with slightly different pulling
coordinates) uses a very high force constant of 12600 kJ/mol/nm^2 and they
have provided no explanation for this.

I have increased simulation time of my windows from 1 ns to 10 ns and I am
thinking of using a higher force constant in one half of my windows where
the pulled group is closer to the reference group and use a lesser
potential in the rest of the windows.
However I am declined to use the 12600 units of force constant as it is
very high and there is no validation. I found some literature using 1000 -
10,000 kJ/mol/nm^2 force constants for proteins.

Any suggestions please ?


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