**From:** CHINDEA Vlad (*vchindea_at_hotmail.com*)

**Date:** Fri Jan 16 2009 - 13:30:26 CST

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Hi Peter

As I mentioned in my first mail I was also suspecting that the missing degrees of freedom are to be blamed. Now I am sure of it, because I have done another simulation with rigidBonds = none for just 10 ps, and although not completely equilibrated the fit was much improved (323 K, as compared to 310 K expected). Also the resulting M-B distribution is well behaved (peak frequency bellow 1). Maybe I have even gone to far as in the tutorial it is mentioned that water should allways be simulated with rigid bonds !

So the message to take home should be the following: for accurate thermodynamic conditions I should allways simulate with rigidBonds = water (at least in the production phase) ? In the tutorial it is not stated explicitely (just that water should allways be simulated rigid, but in the 1-3-box example rigideBonds=all has been used !) . Or is this depending on the system/configuration file actualy used ?

Kind regards

Vlad

* > Date: Thu, 15 Jan 2009 08:22:19 -0600> From: petefred_at_ks.uiuc.edu> To: vchindea_at_hotmail.com> CC: gumbart_at_ks.uiuc.edu; namd-l_at_ks.uiuc.edu> Subject: Re: namd-l: problem in fitting Maxwell-Boltzmann distribution> > 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> > > > On Jan 14, 2009, at 5:08 PM, CHINDEA Vlad wrote:> > > > Hi everybody> > > > I am doing an MD of a protein in a water box with NPT conditions> > (310 K temperature). In order to check the sanity of the simulation> > I have done a temperature estimation by fitting Maxwell-Boltzmann> > distribution to the equilibrated velocity data as explained in the> > tutorial, but although the temperature reported in the log file> > looked quite OK (305-313 K) the result obtained by fitting was just> > 254 K ! What is more strange is that the peak of the kinetic energy> > distribution is higher then 1 (about 1,2-1,3)> > which is statistically (and physically) impossible. Since the> > initial run was just 24 ps I though that maybe I did not> > equilibrated the system enaugh so I restarted the simulation for> > another 30 ps, but the result was about the same both in fitted> > temperature (251 K) and distribution peak. As suggested> > inhttp://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1354.html I> > have corrected also the mathematical expresion of the distribution> > from (kT)^3 (as shown in the tutorial) to (kT)^3/2.> > > > The step size was 2 fs and RigidBonds was on. Is it possible that> > this might have such a deleteriouse effect on the fit due to the> > missing degrees of freedom ? > > > > I understand that I will never get the expected temperature due to> > the finite size of the system but the difference from 250 to 310 K> > seems quite large to me. Please let me know if you need anything> > else in order to see what might be wrong.> > > > Many thanks and kind regards> > Vlad Chindea > >
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