From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri May 20 2016 - 08:07:03 CDT
That's hilarious.
What's even more hilarious is that you replied to the whole list, so I
guess it's public shame for me. Oh well, there is no such thing as bad
publicity, or so I've heard.
:-)
On 20 May 2016 at 15:02, Chris Chipot <chipot_at_ks.uiuc.edu> wrote:
> Mark Zuckerman, c'est Facebook, mon ami... Amitiés,
>
> Chris
>
>
>
> On 5/20/16 7:35 AM, Jérôme Hénin wrote:
>
> Hi,
>
> Yes, that is the book I was talking about.
>
> Here is what I can tell you: to do free energy calculations of the type
> you are mentioning, you need more training, and you probably need an
> advisor who is an expert of this. You're not going to obtain the necessary
> information from a mailing list.
>
> Best,
> Jerome
>
>
>
> On 20 May 2016 at 05:41, sunyeping <sunyeping_at_aliyun.com> wrote:
>
>> I can only find a book named " Statistical Physics of Biomolecules: An
>> Introduction
>> <https://www.amazon.cn/Statistical-Physics-of-Biomolecules-An-Introduction-Zuckerman-Daniel-M/dp/1420073788/ref=sr_1_1?ie=UTF8&qid=1463714615&sr=8-1&keywords=Statistical+Mechanics+of+Biomolecules>"
>> by Daniel M. Zuckerman in the Internet. Is it the one you are to
>> recommend? But before I read the textbook, could you give me some help of
>> my question?
>> I have searched the net and have some ideas that PMF is the free
>> energy at a given reaction coordination. It seems to reflect the energy
>> state of the whole system including the solvent. What I care about is a
>> conformational change occurring in the interface of two large proteins. The
>> residues that are involved in this conformational change constitute a tiny
>> portion of the large protein system so the free energy change related to
>> this conformational change is also tiny relative to the energy of the whole
>> system. So, could ABF method dipict the free energy change during the
>> conformational change?
>>
>> Best regards.
>>
>> ------------------------------------------------------------------
>> From:Jérôme Hénin <jerome.henin_at_ibpc.fr>
>> Time:2016 May 19 (Thu) 15:31
>> To:孙业平 <sunyeping_at_aliyun.com>
>> Cc:namd-l <namd-l_at_ks.uiuc.edu>
>> Subject:Re: namd-l: Some questions on the Deca-Alanine ABF tutorial
>>
>> You need to learn about the meaning of a potential of mean force. There
>> is a good intro book: Statistical Mechanics of Biomolecules, by Mark
>> Zuckerman.
>>
>> Jerome
>>
>> On 19 May 2016 at 03:29, sunyeping <sunyeping_at_aliyun.com> wrote:
>> Hi, Jerome,
>>
>> Thanks. And I still have a concept confusion about ABF. Whether the pmf
>> calculted in the ABF is the potential of the two atoms between which the
>> distance is measured or the potential of the whole Deca-Alanine peptide?
>> If I want to calculate the free energy profile of a set of residues in a
>> protein, should I inculde all these residues in one colvar and apply ABF on
>> certain component of that colvar? For example, if I want to calculate the
>> free energy profile of the interface residues between tho chains, what is
>> the correct way of using ABF?
>>
>> Regards.
>>
>> ------------------------------------------------------------------
>> From:Jérôme Hénin <jerome.henin_at_ibpc.fr>
>> Time:2016 May 18 (Wed) 18:50
>> To:孙业平 <sunyeping_at_aliyun.com>
>> Cc:namd-l <namd-l_at_ks.uiuc.edu>
>> Subject:Re: namd-l: Some questions on the Deca-Alanine ABF tutorial
>>
>> Only set colvarsTrajFrequency to 1 if you need the exact value of the
>> coordinate at each timestep. That is almost never necessary. You get the
>> number of samples per bin in the *.count file.
>>
>> Best,BF
>> Jerome
>>
>> On 18 May 2016 at 10:06, sunyeping < <sunyeping_at_aliyun.com>
>> sunyeping_at_aliyun.com> wrote:
>> Hi, Jerome,
>>
>> Thank you.
>> You said "there is one ABF sample per MD timestep". Then to get the
>> sample numbers for each distance （ξ） value, do we have to set the colvarsTrajFrequency
>> to 1?
>> All the best!
>> ------------------------------------------------------------------
>> From:Jérôme Hénin < <jerome.henin_at_ibpc.fr>jerome.henin_at_ibpc.fr>
>> Time:2016 May 17 (Tue) 23:33
>> To:namd-l <namd-l_at_ks.uiuc.edu>; 孙业平 < <sunyeping_at_aliyun.com>
>> sunyeping_at_aliyun.com>
>> Subject:Re: namd-l: Some questions on the Deca-Alanine ABF tutorial
>>
>> Hi,
>>
>> On 16 May 2016 at 11:19, sunyeping <sunyeping_at_aliyun.com> wrote:
>> Dear all,
>>
>> I am studying the Deca-Alanine ABF tourial and ABF method. I have
>> finished the 5 ns run of the tutorial but I have several questions on the
>> analysis of the results. In the tutorial the figure 1 in page 10 gives the
>> results of the potential (delta A（ξ））as a function of the distance （ξ）.The
>> range of the delta A（ξ）is from around -4 to 23 kcal/mol. The tourial
>> says that convergence usually occurs within 5 ns and one of the criteria of
>> convergence is that the pmf does not vary any more. It seems that we should
>> exam the change of pmf against time to judge wether the simulation has
>> converged. Is there a output file that gives the pmf vs time result?
>>
>> That file is only saved if you set the historyFreq parameter.
>>
>> In my output pmf files, the delta A（ξ）ranges from about 0.2 to 39
>> kcal/mol, which is different from the tutorial. Is this OK? Another
>> question is, in the figure 1 in the tourial, the inset shows the number of
>> samples at each distance. How is the number of samples counted? Is it
>> counted from the traj files? However, there are only 10000 frames in the
>> traj file, while the number of samples in the inset figure are more than
>> 1×105 at each distance. Where does these numbers come from?
>>
>> The trajectory file has one value per colvarsTrajFrequency steps, whereas
>> there is one ABF sample per MD timestep.
>>
>> The tutorial claims that the unfolding of deca-alaline is reversible
>> and the different conformational states of the peptide chain are visited frequently.
>> However, in my simulation, the unfolded peptide revert to the helix only in
>> the last frame? Is this correct?
>>
>> This is correct on average and for long trajectories. You may see it by
>> running more trajectories with the same parameters.
>>
>> The NAMD user's guide says that reconstructing multidemensional free
>> energy surface requires abf_integrate command. But I cannot find it in the
>> NAMD binary packages. where is this command implemented?
>>
>> It's provided as source code only. This is explained here:
>>
>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2009-2010/3491.html
>>
>> Best,
>> Jerome
>>
>>
>>
>>
>>
>>
>
>
> --
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> Theoretical and Computational Biophysics Group
> 3047 Beckman Institute for Advanced Science and Technology
> University of Illinois at Urbana-Champaign
> 405 North Mathews
> Urbana, Illinois 61801 Phone: (217) 244-5493
>
> E-mail: chipot_at_ks.uiuc.edu
> Christophe.Chipot_at_Univ-Lorraine.fr
> Web: http://www.ks.uiuc.edu/~chipot
> http://www.lia-uiuc.cnrs.fr
>
> It is hard for France to maintain a thirty-five-hour workweek when
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> Thomas L. Friedman
> _______________________________________________________________________
>
>
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