Re: Some questions on the Deca-Alanine ABF tutorial

From: Pardis Tabaee (pardis.tabaee.d_at_hotmail.co.uk)
Date: Fri May 20 2016 - 10:01:13 CDT

I think it would be the same as running any other simulation with namd, and the 10000 is the number of timesteps for the ABF simulation in your case, so depending if you have 2fs/tstep specified somewhere, that would mean that 10000 is 20000 fs, therefore 20 ps, therefore 0.02 ns?

I presume?

________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Jrme Hnin <jerome.henin_at_ibpc.fr>
Sent: 18 May 2016 11:49
To: sunyeping
Cc: namd-l
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,
Jerome

On 18 May 2016 at 10:06, sunyeping <sunyeping_at_aliyun.com<mailto: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 (?) value, do we have to set the colvarsTrajFrequency to 1?
All the best!
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From:Jrme Hnin <jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>>
Time:2016 May 17 (Tue) 23:33
To:namd-l <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>; ??? <sunyeping_at_aliyun.com<mailto: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<mailto: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(?))as a function of the distance (?).The range of the delta A(?)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(?)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 1105 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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