Re: FEP - one long simulation vs many short ones

From: Mauricio Carrillo Tripp (
Date: Fri Jul 01 2005 - 18:27:24 CDT

I believe the idea is to go from lambda=0 to lambda=1 (or the opposite)
in a 'smooth' way.
If I understand correctly by what you describe, you start from a
with lambda=0.5, for all points in between 0 and 1!? That wouldn't give you
a smooth transformation
from lambda=0.5 to lambda=1 (or 0), or any points in between but maybe only
those with lambda close to 0.5
Then again, I might be wrong. I've never done any FEP, just read the theory,
anybody, please correct me if I am wrong...

On 7/1/05, Floris Buelens <> wrote:
> Hello,
> I have a question about my approach to running FEP
> simulations.
> I understand the normal approach is to run a single
> simulation starting off at lambda=0 or 1 and changing
> lambda (in discrete steps, with an equilibration
> period after each change) over the course of a single
> simulation.
> With my department's computer system, however, it's
> far more efficient to run many shorter, unconnected
> simulations at different values of lambda. Currently,
> I set up the system and generate a single starting
> point for the simulations, by running 100ps at lambda
> 0.5. I then run 80 unconnected simulations restarting
> from this point, at different values of lambda (each
> with 40ps equilibration before data collection).
> By running unconnected simulations like this, I escape
> any penalty from parallel scaling, and I can run a
> total of ~32ns in 36 hours. If I were to attempt 32ns
> in a single simulation, the fastest I could hope for
> with my setup would be around 9 days, which is
> completely impractical.
> I wanted to ask if there are any dangers in running
> FEP like this? Is this a common approach? I guess I
> risk problems in the equilibration from the lambda 0.5
> starting point to the test value. However perhaps I
> gain something by cutting out any general 'drift' that
> would inevitably arise over a long simulation, which
> in turn reduces or bypasses the issue of hysteresis
> associated with a 'directional' simulation.
> thanks for your attention,
> Floris Buelens
> Crystallography, Birkbeck College
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Mauricio Carrillo Tripp, PhD
Department of Chemistry
Wabash College

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