Robert Johnson wrote:
Hello Pascal,
I'm not sure I can really comment on (1), but the reason why your
energy gap decreases in (2) is because the energy fluctuations in your
system increase as you raise the temperature. For example, at low
temperatures your potential energy distributions will be sharply
peaked about the average value. However, as you increase the
temperature, the peak will broaden because of the increased thermal
fluctuations. As a result, you will have more overlap between your
potential energy distributions at higher temperature.
What Bob says is true, but Pascal was talking about
the gap between average potential energies
which is not directly dependent of the shape of the distribution.
On Tue, May 6, 2008 at 9:50 AM, <[EMAIL PROTECTED]> wrote:
Dear community,
I am performing some REMD tests with the trp-cage peptide. In order to figure
out the optimal temperature distribution ensuring similar exchange
probabilities
at every temperature, I have performed short MD runs at increasing
temperatures,
with a run every 5K from 300K to 500K. If I plot the average potential energy
as
a function of temperature, I obtain the following trend:
1) For NPT, the gap between average potential energies progressively increases
with equal increments of temperature.
2) For NVT, the gap between average potential energies progressively decreases
with equal increments temperature.
You seem to be in qualitative agreement with Figure 1 of
M Marvin Seibert, Alexandra Patriksson, Berk Hess and David van der
Spoel (2005).
Reproducible Polypeptide Folding and Structure Prediction using
Molecular Dynamics Simulations.
Journal of Molecular Biology, 354(1):173-183
Figures 4 and 5 of
Daniel Sindhikara, Yilin Meng and Adrian E Roitberg (2008).
Exchange frequency in replica exchange molecular dynamics.
Journal of Chemical Physics, 128(2):024103.
show linearity for a wide range of temperatures, however they use a GB
solvent model.
I also read a very interesting paper on this issue:
Alexandra Patriksson and David van der Spoel, A temperature predictor for
parallel tempering simulations Phys. Chem. Chem. Phys., 10 pp. 2073-2077 (2008)
The temperature predictor works with a set of parameters obtained from a number
of simulations of different proteins at different temperatures. Among the test
proteins, the Trp-cage peptide is also used, but the authors describe a linear
function for average potential energy as a function of temperature. However,
this result was obtained in the 284 to the 330K range, and my results also
appear linear in this domain.
As far as I understand, potential energy should scale with the number of
degrees
of freedom f and temperature T:
Epot_{avg} ~= f k_B T (k_B is Boltzmann's constant)
Could anybody explain to me why the relation I obtain in 1) and 2) here above
are not linear? Is the linearity broken from a higher threshhold temperature,
for which force field parameters are not designed, onwards?
How non-linear are they? I'd expect that such non-linearity is useful
evidence of the non-transferability of force fields to high
temperatures. All of my REMD simulations use a maximum T around
350-360K, so I figure my average energies won't say much of anything.
I'd expect some serious distortion in Epot_{avg} for NVT at high T,
because now the pressure is far too large to match the parameterization
conditions. This forms much of the argument for doing NPT-REMD, as made
in Seibert, et al. above.
Mark
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