From: Chris Chipot (chipot_at_ks.uiuc.edu)
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.
Regards,
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
E-mail: chipot_at_ks.uiuc.edu
Christophe.Chipot_at_Univ-Lorraine.fr
Web: http://www.ks.uiuc.edu/~chipot
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