From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Jun 25 2007 - 14:30:51 CDT

1) Each SMD simulation started from an equilibrated point. To
minimize the number of equilibration simulations needed, they pulled
in opposite directions from each starting point.

2) I think so. I wouldn't say they had reduced work though; the
highest point occurs in one of the reverse directions.

3) The procedure in the deca-alanine tutorial is the same as that in
the paper in Eq. 7, both using the cumulant expansion of the average
work. Eq. 8 is just a more complicated way of calculating <W> and
<W^2>.

On Jun 23, 2007, at 9:23 PM, Sting wrote:

> Hi JC Gumbart,
> sorry to disturb you again. As your suggestion, I read the paper
> of Jensen et al.carefully, and in this paper I still have some
> confusion:
> 1. Why they performed SMD in two directions?
> 2. It seems the most forces obtained from the inverse direction
> are negative and these had reduced the works computed in Fig 2.b.
> Do the negative values derive from the 'negative' direction?
> 3. In this paper, a formula 8 was used, but I can not have any clue
> from the tutorial 10Ala_tutor.
> Since both the papers are from your group, they really puzzle me.
>
>
> Thank you a lot!
> ======= =======
>
>> I can attempt to answer but someone may correct me:
>>
>> 1) I'm pretty sure it would be the former, although it seems at least
>> in our group that people calculate it slightly differently (but I am
>> pretty sure both ways are equivalent). Please see some papers from
>> our group for more specifics on this point (I'm looking at right now
>> for instance Jensen et al. "Energetics of glycerol conduction through
>> aquaglyceroporin GlpF").
>>
>> 2) The PMF is a force profile where as the activation energy is the
>> amount of energy required to overcome the initial barrier. I do not
>> know if the free energy of activation is different or not. I have
>> never calculated a PMF myself, but one way to judge would be the size
>> of the activation energy. 100 kJ/mol (~25 kcal/mol) does seem a bit
>> large however and would likely only proceed if something else
>> provided the energy or a conformational change took place (for
>> comparison, thermal energy is only about 0.6 kcal/mol). One point I
>> will make is that calculating accurate PMFs requires good sampling,
>> so if you only ran one trajectory, it probably accumulated a large
>> amount of irreversible work. Additional trajectories, appropriately
>> averaged using Jarzynki's equality (again, papers from our group
>> would be most helpful), may yield a lower number.
>>
>> More experienced people may feel free to chime in here. In any case,
>> good luck!
>>
>>
>> On Jun 18, 2007, at 11:00 PM, Sting wrote:
>>
>>> Hi all:
>>>
>>> I have performed a series of SMD with a constant velocity of 10
>>> Γ/
>>> ns to force a ligand release from the binding pocket and try to
>>> reconstruct the PMF, and I have some problem as follow:
>>>
>>> 1. How to compute the works done during the process? Should it be:
>>> The displacement of ligand*applied Force or The displacement of the
>>> moving point which drag the ligand ?
>>>
>>> 2. What is the diffrence between the PMF and the Activation Energy
>>> as well as that between it and the Free Energy of Activation, and
>>> how to verify a reasonable PMF?
>>>
>>>
>>> I really need someone to help me. Thank you in advance!
>>>
>>>
>>>
>>>
>>>
>>> γγγγγγγγSting
>>> γγγγγγγγstg1979_at_emails.bjut.edu.cn
>>> γγγγγγγγγγ2007-06-15
>>
>>
>
> = = = = = = = = = = = = = = = = = = = =
>
>
> γγγγγγγγθ΄
> η€ΌοΌ
>
>
> γγγγγγγγSting
> γγγγγγγγstg1979_at_emails.bjut.edu.cn
> γγγγγγγγγγ2007-06-24
>

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