RE: Equilibration for a reverse FEP run

From: Matthew Ralph Adendorff (mraden_at_mit.edu)
Date: Thu Apr 23 2015 - 10:16:08 CDT

Hi Chris

Thank you for the very prompt response. I'll restart from the terminal lambda state with appropriate equilibration.

Best,

Matthew

Matthew Adendorff
PhD Candidate
Laboratory for Computational Biology and Biophysics
Department of Biological Engineering
Massachusetts Institute of Technology
________________________________________
From: Chris Chipot [chipot_at_ks.uiuc.edu]
Sent: 23 April 2015 11:04 AM
To: namd-l_at_ks.uiuc.edu; Matthew Ralph Adendorff
Subject: Re: namd-l: Equilibration for a reverse FEP run

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 -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

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