[gmx-users] REMD: average potential energy as a function of temperatue

[pascal.baillod at epfl.ch]

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	pascal.baillod at epfl.ch
Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
CH-1015 Lausanne	
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