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.
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?
Thanks a lot in advance!!
Pascal
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Pascal Baillod (PhD student)
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Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry [EMAIL PROTECTED]
Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch
CH-1015 Lausanne
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