From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jan 16 2009 - 13:48:27 CST
CHINDEA Vlad wrote:
> Hi Peter
> As I mentioned in my first mail I was also suspecting that the missing
> degrees of freedom are to be blamed.
Yes; my point was simply that even with rigidbonds it is easy to do the
analysis you want by using the appropriate number of degrees of freedom.
> 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) ?
One ought to use rigidbonds water with TIP3P water since it is supposed
to be a rigid water model. rigidbonds all is optional; there's a good
deal more debate over how useful it is to make solute bonds involving
hydrogen rigid, since it allows you to use 2 fs timesteps but requires
the use of a (slower) iterative solver for the constraints (although all
of the constraints have gotten much faster in the cvs version of namd,
so this is now less of a problem), and over what effect (if any)
rigidbonds all has on the resulting dynamics.
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
>> 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.
>> > > 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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