[gmx-users] Pressure and compressibility

Janne Hirvi janne.hirvi at joensuu.fi
Mon Jan 2 15:24:31 CET 2006


I have tried to simulate bulk polymers over a range of temperatures from melted
via rubbery to glassy state. The Berendsen algorithm have been used temperature
and pressure couplings. 

First "separate" simulations at different temperatures were made using isotropic
pressure coupling with time constant 0.5 ps and different compressibilities for
different states/temperatures. Densities were more or less stabilized, but
averaged pressure (averaged for 1000 ps) showed positive deviation of dozens of
bars from the target pressure (1 bar) for simulations at low temperatures with
low compressibility (5.0E-07 1/bar).

Recently I have used simulated annealing procedure with anisotropic pressure
coupling with same 0.5 ps time constant and compressiblity of 5.0E-06 1/bar for
whole range of temperatures. The results are more or less equal, but still the
average pressure for almost every temperature deviates from the target pressure
couple of bars (averaged for 500 ps).

1) Are these deviations from the target pressure normal or should I change

2) How about compressibility? Can I use same value of compressibility for all

3) If I decrease the value of compressibility, should I do something for the
time constant too to make pressure stabilize more better/quicker?    

Thanks for any help or comments! 


Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi

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