Re: FEP - one long simulation vs many short ones

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Sat Jul 02 2005 - 12:13:51 CDT

Hi,

I am not understand how you calculate free energy difference between
0.5 and any other points, like 0.8. How did you get the total difference
between 0 and 1?

Make sure that step size for lambuda is as small as possible because
enough sampling is possible only when d(lambuda) is small.

Wei Chen

Floris Buelens <floris_buelens_at_yahoo.com>:

> 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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