**From:** Peter Freddolino (*petefred_at_ks.uiuc.edu*)

**Date:** Thu Jan 15 2009 - 08:22:19 CST

**Next message:**Peter Freddolino: "Re: dielectric parameter?"**Previous message:**CHINDEA Vlad: "RE: problem in fitting Maxwell-Boltzmann distribution"**In reply to:**CHINDEA Vlad: "RE: problem in fitting Maxwell-Boltzmann distribution"**Next in thread:**CHINDEA Vlad: "RE: problem in fitting Maxwell-Boltzmann distribution"**Reply:**CHINDEA Vlad: "RE: problem in fitting Maxwell-Boltzmann distribution"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Did you use the correct number of degrees of freedom in your analysis?

You mentioned that you use rigidbonds; a rigid water molecule has only 6

degrees of freedom, and every bond involving a hydrogen in your solute

is also constrained (if you're using rigidbonds all) and removes a

degree of freedom. You can find a count of the number of degrees of

freedom in your logfile under the STRUCTURE SUMMARY heading.

Best,

Peter

CHINDEA Vlad wrote:

*> You are right about the tutorial (actually I am using the Windows
*

*> version). I took for granted what was written on the list also due to
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*> the fact that with the ^3/2 factor the fit was emproved a little bit.
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*> With the correct ^3 factor the fitted temperature is only 199 K ! And
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*> now also the theoretical M-B distribution peaks at over 1,0 probability
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*> ! Of course I have normalized the frequency by dividing the counts in
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*> every bin to the total area under the histogram, as explained in the
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*> tutorial.
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*>
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*> Best regards
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*> Vlad
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*>
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*>
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*> ------------------------------------------------------------------------
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*>
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*> CC: namd-l_at_ks.uiuc.edu
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*> From: gumbart_at_ks.uiuc.edu
*

*> Subject: Re: namd-l: problem in fitting Maxwell-Boltzmann distribution
*

*> Date: Wed, 14 Jan 2009 19:00:12 -0600
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*> To: vchindea_at_hotmail.com
*

*>
*

*> Actually the tutorial is not wrong. In step 20 on page 40 of the
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*> current Unix/Mac version of the NAMD tutorial, there is an a0^3, where
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*> a0 = kbT. However, this a0^3 is under the square root along with Pi,
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*> making it 3/2 overall. Will changing this correct your fit?
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*>
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*> Also, did you normalize your distribution? This is an option in the
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*> Histogram window of xmgrace. Not having done that may explain why you
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*> get values greater than 1.
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*>
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*>
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*> On Jan 14, 2009, at 5:08 PM, CHINDEA Vlad wrote:
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*>
*

*> Hi everybody
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*>
*

*> I am doing an MD of a protein in a water box with NPT conditions
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*> (310 K temperature). In order to check the sanity of the simulation
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*> I have done a temperature estimation by fitting Maxwell-Boltzmann
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*> distribution to the equilibrated velocity data as explained in the
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*> tutorial, but although the temperature reported in the log file
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*> looked quite OK (305-313 K) the result obtained by fitting was just
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*> 254 K ! What is more strange is that the peak of the kinetic energy
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*> distribution is higher then 1 (about 1,2-1,3)
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*> which is statistically (and physically) impossible. Since the
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*> initial run was just 24 ps I though that maybe I did not
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*> equilibrated the system enaugh so I restarted the simulation for
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*> another 30 ps, but the result was about the same both in fitted
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*> temperature (251 K) and distribution peak. As suggested
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*> inhttp://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1354.html I
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*> have corrected also the mathematical expresion of the distribution
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*> from (kT)^3 (as shown in the tutorial) to (kT)^3/2.
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*>
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*> The step size was 2 fs and RigidBonds was on. Is it possible that
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*> this might have such a deleteriouse effect on the fit due to the
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*> missing degrees of freedom ?
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*>
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*> I understand that I will never get the expected temperature due to
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*> the finite size of the system but the difference from 250 to 310 K
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*> seems quite large to me. Please let me know if you need anything
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*> else in order to see what might be wrong.
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*>
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*> Many thanks and kind regards
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*> Vlad Chindea
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*>
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**Next message:**Peter Freddolino: "Re: dielectric parameter?"**Previous message:**CHINDEA Vlad: "RE: problem in fitting Maxwell-Boltzmann distribution"**In reply to:**CHINDEA Vlad: "RE: problem in fitting Maxwell-Boltzmann distribution"**Next in thread:**CHINDEA Vlad: "RE: problem in fitting Maxwell-Boltzmann distribution"**Reply:**CHINDEA Vlad: "RE: problem in fitting Maxwell-Boltzmann distribution"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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