Re: FEP restart?

From: Chris Harrison (
Date: Wed Mar 11 2009 - 19:53:09 CDT


I can't think of a reason an FEP could not be restarted. I think you
maybe confusing the way FEP works inside NAMD with the way one of the
example tcl scripts works that allows you to do a full series of lambda values in a single NAMD config script. Can you send your namd config file?


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
Christopher Hartshorn <> writes:
> Date: Wed, 11 Mar 2009 17:34:59 -0700
> From: Christopher Hartshorn <>
> To:
> Subject: namd-l: FEP restart?
> Return-Path:
> Message-Id: <>
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> 	autolearn=unavailable version=3.1.7-0+tcb1
> Hello all.  Recently, my dept. lost power during a snow storm here in  
> Pullman.  Unfortunately, I did not have a few of the computers on a  
> power backup system and two sims were stopped before they had ripened,  
> if you will.
> One of the sims was an FEP calculation, which brings me to my question  
> of can an FEP be restarted?  I had the restart feature on, of course,  
> for the usual every 1000 steps, but the more I think about it the more I 
> wondered whether this matters.  If my last restart file was from the  
> 55000 n step of lambda step .50 to .54 (there are 80K total n steps/ 
> lambda step) then my restart would be in the middle of the n iterations 
> and I could not start from this point (as far as I understand, at least). 
>  I can only restart, I think, from the beginning of the lambda step (as 
> in at the n=0 point).  Thus, am I correct in my thinking about this, that 
> I need to rerun the entire FEP because I do not have a restart point at 
> the beginning of some lambda step?  And, on that same note for the 
> future, should I set my restart step number to the same as my n 
> iterations number (e.g. restart=80K steps if n steps=80K) so that each 
> restart file set will be only at the beginning of the lambda step?
> Thank you very much for any and all answers.
> Best,
> Chris

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