Re: Equilibration for a reverse FEP run

From: Chris Chipot (
Date: Thu Apr 23 2015 - 10:04:32 CDT

Hello Matthew,

if this is a continuation of the forward run, there is no real need to
re-equilibrate. Suffice to restart in the other direction, assuming
that your have an appropriate number of equilibration steps per
stratum, or λ-state, to eliminate any possible Hamiltonian lag.

Thanks you for the kind comment on our tutorials.


Chris Chipot

On 4/23/15 9:54 AM, Matthew Ralph Adendorff wrote:
> Good day,
> Before running a forward FEP calculation, I know one equilibrates the system with something similar to:
> runFEP 0.0 0.0 0.0 $numSteps
> Before the reverse calculation, should one perform a similar equilibration with:
> runFEP 1.0 1.0 0.0 $numSteps
> or would this adversely affect the calculation?
> Best regards and thank you for the excellent tutorial,
> Matthew
> Matthew Adendorff
> PhD Candidate
> Laboratory for Computational Biology and Biophysics
> Department of Biological Engineering
> Massachusetts Institute of Technology

Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
3047 Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
405 North Mathews
Urbana, Illinois 61801                            Phone: (217) 244-5493
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