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

**Date:** Fri Nov 22 2013 - 12:09:37 CST

**Next message:**nan li: "Interaction energy definition"**Previous message:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**In reply to:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Next in thread:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Reply:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Jerome,

I was using "minimize" incorrectly.

I meant for each window I have 5000 steps of equilibration followed by

10,000 steps of data collection.

So I should try increasing the equilibration steps.

thanks,

Shyno

On Fri, Nov 22, 2013 at 12:01 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:

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

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

*> 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
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*>> free
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*>> > energy.
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*>>
*

*>> In general I wouldn't recommend minimizing between windows. You have to
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*>> thermalize to room temperature again every time, and discard the additional
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*>> equilibration time.
*

*>>
*

*>> > So just to be clear, in the previous message by saying "increase the
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*>> > 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
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*>> 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
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*>> exponenials of deltaGs.
*

*>>
*

*>> Jerome
*

*>>
*

*>>
*

*>
*

*>
*

*> --
*

*> Shyno Mathew
*

*> PhD student
*

*> Department of Chemical Engineering
*

*> Columbia University
*

*>
*

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

**Next message:**nan li: "Interaction energy definition"**Previous message:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**In reply to:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Next in thread:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Reply:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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