From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Fri Nov 22 2013 - 12:09:37 CST
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
> 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
>
-- Shyno Mathew PhD student Department of Chemical Engineering Columbia University
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