# Re: Some questions on the Deca-Alanine ABF tutorial

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed May 18 2016 - 05:49:56 CDT

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,
Jerome

On 18 May 2016 at 10:06, sunyeping <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>
> Time:2016 May 17 (Tue) 23:33
> To:namd-l <namd-l_at_ks.uiuc.edu>; 孙业平 <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
>
>
>

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