From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Mar 02 2012 - 10:51:16 CST
Just as a follow-up on this topic: I'm not sure exactly where the problem
occurred in terms of calculating the temperature of the flexible protein
atoms, as it seems that should have just been fitting the kinetic energies
of all the protein atoms (which had no constraints) to a boltzmann
distribution after calculating them from KE=0.5mv^2, but somehow my
rudimentary understanding of physics caused a mishap.
Anyway, the point in the end is that, using Jim Phillips updated NAMD
executable that prints out separate water and nonwater temperatures,
illustrates that nothing was wrong at all, with the average temperature for
the non-water atoms being less than 5 K higher than the water, and given
the smaller number that is totally expected.
Sorry for the confusion and false alarm.
On Thu, Mar 1, 2012 at 4:06 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> Hi Jim,
> Thanks a lot for the answers. Just as a point of clarification, I never
> tested turning "langevinHydrogen off" and leaving everything flexible, I
> only noticed the problem with it off and rigidBonds water, and then saw a
> corrected behaviour with it either on, or left off but then rigidBonds all.
> Thanks also for clearing up the matter of the oxygens, it seems like it
> may be the case that the whole system is heating up then and there isn't a
> difference between solute and solvent. It would still be the case that
> having langevinHydrogen off with rigidBonds water while having a flexible
> hdyrogenated solute would be bad for things, but at least uniformly bad.
> On Thu, Mar 1, 2012 at 3:47 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>> Hi all,
>> I should have some code to separate water and non-water temperatures
>> checked in tonight.
>> I still need to run more tests, but my current line of thought is that
>> with "langevinHydrogen off" and "rigidBonds water" the protein has a lower
>> level of temperature coupling per degree of freedom than the water, the
>> protein will conserve energy worse than the water because it has
>> high-frequency bonds to hydrogens, and the temperature coupling is turned
>> off specifically on those high-frequency bonds most likely to heat.
>> That said, the reported temperature difference seems unlikely, as the
>> above explanation would suggest that "langevinHydrogen off" without rigid
>> bonds should produce a similarly high temperature for the whole system. I
>> don't see how "rigidBonds water" would cause the protein to heat more.
>> Again, this is all speculation. Tests are running.
>> On Tue, 28 Feb 2012, Aron Broom wrote:
>> Dear NAMD users,
>>> I've looked around on the mailing list and couldn't find a clear answer
>>> as to whether or not it is supposed to be ok to use rigidBonds water (say
>>> with TIP3P) but then leave the solute (say a protein) flexible with a 1
>>> timestep and langevinHydrogen off in order to save on calculating
>>> collisions with the large number of rigid hydrogens in the sample. It
>>> might seem like one should not use langevinHydrogen off as long as there
>>> are any flexible hydrogens, but several sources, including an NAMD
>>> have exactly this setup.
>>> Well, I believe I have confirmed that you should NOT do this. In looking
>>> at a 60ns simulation of ~2000 protein atoms in an ~100,000 water atom
>>> and determining the temperature of the non-rigid parts of the system by
>>> calculating their kinetic energies (KE=0.5mv^2), binning them, and then
>>> fitting to the boltzmann distribution ( y = (2/sqrt(Pi * (KbT)^3 )) *
>>> sqrt(x) * exp(-x/KbT) ), I find that the temperature of the whole system
>>> fine (set to 298 K, and comes out on average at 297 K), but the
>>> of the protein alone is ~20-25 K higher than the surrounding solvent
>>> throughout the simulation.
>>> This is a big problem, especially for studying ligand binding, and I
>>> imagine for anything having a 20-25 K difference across the
>>> interface is bad, not to mention just being incorrect.
>>> I tested running an extra 4ns from the end of my 60 ns, with two changes
>>> NAMD parameters:
>>> 1) just turn langevinHydrogen on, which comes with a 5% performance
>>> penalty, and
>>> 2) leave langevinHydrogen off, but change rigidBonds water to rigidBonds
>>> all, and change from a 1 fs timestep to a 2 fs timestep, in which you
>>> ~30% performance, but some people are sceptical of the results.
>>> Both of these changes alone are capable of bringing the system back to a
>>> reasonable configuration in which the protein and solvent have
>>> approximately the same temperatures (the protein was still slightly
>>> (~5 K, but perhaps a gamma of 1/ps is not fast enough to see complete
>>> equilibrium in 4ns).
>>> Has anyone else seen this and can confirm that the setup of using
>>> ridigBonds water and langevinHydrogen off are not to be used together
>>> you have a solute that has hydrogens, despite this being somewhat common
>>> practice? If anyone wants to test the temperatures of various parts of
>>> their systems from existing *.vel files, I just followed the instructions
>>> on this page (
>>> but note that the units in the .vel files must changed since this was
>>> written, so you'll have to convert amu to kg, and angstrom/ps to m/s, and
>>> then use the correct boltzmann constant for those units.
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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