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

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Tue Dec 03 2013 - 17:12:43 CST

Hello Jerome,
Is there a way to make sure my system is equilibrated at each strata?
Currently, I do 10000 steps of equilibration followed by 10000 steps of
data collection. But I am not sure 10,000 steps of equilibration is enough?
Also, what method/algorithm namd uses to do FEP?
I read BAR is another method to calculate free energy.
Since the ParseFEPplugin was showing us some errors, we are trying to write
a script that calculates BAR.

thanks,
Shyno

On Fri, Nov 22, 2013 at 1:09 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:

> 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--001a11c3f0420f27e804eca96f30--

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