From: Pardis Tabaee (pardis.tabaee.d_at_hotmail.co.uk)
Date: Fri May 20 2016 - 09:52:09 CDT
Hi,
To output a trajectory every timestep you need to change the section in the namd configuration file ($namd.conf) where:
restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 500
outputEnergies 200
outputPressure 200
You could either change just the dcdfreq, (it's the trajectory frequency), to output every 1, by just doing:
dcdfreq 1
or you can change all of them and set them to 1, but it can happen that you "use" too much space. It's up to you on what you need to do.
All the best,
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Jérôme Hénin <jerome.henin_at_ibpc.fr>
Sent: 20 May 2016 13:35
To: sunyeping
Cc: namd-l
Subject: Re: namd-l: Some questions on the Deca-Alanine ABF tutorial
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<mailto: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.
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From:Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>>
Time:2016 May 19 (Thu) 15:31
To:孙业平 <sunyeping_at_aliyun.com<mailto:sunyeping_at_aliyun.com>>
Cc:namd-l <namd-l_at_ks.uiuc.edu<mailto: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<mailto: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.
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From:Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>>
Time:2016 May 18 (Wed) 18:50
To:孙业平 <sunyeping_at_aliyun.com<mailto:sunyeping_at_aliyun.com>>
Cc:namd-l <namd-l_at_ks.uiuc.edu<mailto: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<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 （ξ） value, do we have to set the colvarsTrajFrequency to 1?
All the best!
------------------------------------------------------------------
From:Jérôme Hénin <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>>; 孙业平 <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（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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