**From:** Shyno Mathew (*sm3334_at_columbia.edu*)

**Date:** Fri Nov 22 2013 - 11:01:18 CST

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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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