Re: FEP calculations: optimizing the dlambda, number of steps

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Fri Nov 22 2013 - 11:01:18 CST

thanks again Jerome. Sorry to bother with multiple questions.
Here is how the FEP section of my .conf file looks like (I saw it in one of
the FEP tutorials).
So for each window it does 5000 step minimization followed by 10,000 step
run. What you are suggesting is just do minimization at the very first
window only?

alch on
alchType FEP
alchFile 04collab_wet.fep
alchCol B
alchOutFile 05collab.fepout
alchOutFreq 100
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 5.0
alchDecouple off
alchEquilSteps 5000

set Lambda0 0.0
set dLambda 0.05
while {$Lambda0 < 1.0} {
  alchLambda $Lambda0
  set Lambda0 [expr \$Lambda0 + \$dLambda]
  alchLambda2 $Lambda0
  run 15000
}

thanks,
Shyno

On Fri, Nov 22, 2013 at 11:49 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> ----- Original Message -----
> > Thanks for the reply Jerome.
> > Now, for each window I have 5000 minimization followed by 10000 steps. I
> > did try going to 10^6 steps, but didn't give significant difference in
> free
> > energy.
>
> In general I wouldn't recommend minimizing between windows. You have to
> thermalize to room temperature again every time, and discard the additional
> equilibration time.
>
> > So just to be clear, in the previous message by saying "increase the
> > sampling time for just those two by running extra simulations" you meant
> > going to smaller dlambda values between 0.45 and 0.55?
>
> I meant running more MD for the same lambda and dlambda values.
>
> > Also, does it make sense to do FEP just between 0.45 and 0.55 and then
> use
> > it with data for all other windows?
>
> Yes, you can merge any amount of data from separate runs. How to do it
> properly depends on what free energy estimator you use. For the FEP
> estimator, it's just a matter of taking the log of a weighted average of
> exponenials of deltaGs.
>
> Jerome
>
> 

-- 
Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University

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