ail.com> wrote:
> Hello,
> R
> How are you constructing the PMF? Are you using SMD and calculating the PMF
> with the Jarzynski equation? Are you using umbrella sampling? If you are
> using SMD with Jarzynski averaging, you should include every single
> trajectory in your average to get the total PMF. You can find likely the
> "best" pathway, or the one that corresponds closest to the PMF, by comparing
> the potential energy surface of each simulation with the average PMF
> obtained from averaging all of them, and whichever one follows that curve
> closest will probably be a good choice.
>
> Hope this helps,
> Jason
>
> On Tue, Aug 17, 2010 at 7:00 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
>>
>> Dear All,
>>
>>
>>
>> I would like to stuy the drug dissociation pathway from a receptor.
>>
>>
>>
>> I tried to use PMF to discript the distance between the drug and the active
>> site. I noted that the path is sensitive to the atoms used to define the
>> distance restraint.
>>
>>
>>
>> If I want to chose the most important drug dissociation pathway for further
>> discussion, is the one with the lowestest energy should be used? If not,
>> what is the requirement should be used to chose the right pathway?
>>
>>
>>
>> best regards,
>>
>>
>>
>> Cat
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Wed Aug 18 2010 - 01:00:03 PDT
