From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Tue Dec 10 2013 - 10:28:10 CST
Dear all,
I would like to confirm the FEP part in my .conf file is correct?
1. Here is how it looks like for the forward FEP :
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 $Lambda0
run 15000
}
2. Now for the reverse FEP everything is same except the following:
set Lambda0 1.0
set dLambda -0.05
while {$Lambda0 > 0.0}
thanks in advance for your help,
best,
Shyno
On Tue, Dec 3, 2013 at 6:12 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:
> 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. 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
>>
>
>
>
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
>
-- Shyno Mathew PhD student Department of Chemical Engineering Columbia University
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