From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Fri Jul 01 2005 - 07:07:14 CDT
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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