[gmx-users] Parrinello-Rahman barostat: temperature and potential energy depend on tau_p
Andrey Frolov
andrey.i.frolov at mail.ru
Tue Jan 7 12:37:52 CET 2014
Dear GMX-Users,
Still no reply. I repost the questions. Any suggestions?
Andrey Frolov wrote
>
> I am simulating pure supercritical CO2 fluid in NPT ensemble. Reference
> temperature is 308.15K. I use “sd” (Langevin dynamics) to control
> temperature with tau_t = 2ps. After 100 ps of equilibration in NPT with
> Berendsen thermostat, I run production simulation of 10 ns with
> Parrinello-Rahman barostat. I checked several values of tau_p (from 2 to
> 100 ps) with the compressibility set to 4.5e-5 bar^-1.
>
> 1) Temperature as given in the mdrun log file and edr files is higher than
> the reference temperature. Moreover, the temperature depends on tau_p: the
> larger tau_p the lower the resulting T:
> tau_p Quantity Average
> Err.Est. RMSD Tot-Drift
> 2.0 Temperature 437.688
> 6.8 82.8611 5.83615 (K)
> 5.0 Temperature 321.009
> 0.49 10.1346 1.51488 (K)
> 10.0 Temperature 314.071
> 0.18 7.06755 0.588431 (K)
> 15.0 Temperature 312.508
> 0.2 6.48075 0.725419 (K)
> 20.0 Temperature 311.831
> 0.12 6.48166 -0.0137431 (K)
> 25.0 Temperature 311.783
> 0.093 6.48474 -0.713862 (K)
> 30.0 Temperature 311.289
> 0.099 6.41436 0.764874 (K)
> 50.0 Temperature 311.392
> 0.15 6.5612 0.585978 (K)
> 100.0 Temperature 311.278
> 0.11 6.51524 0.488872 (K)
>
> What could cause such behavior? Could it be that the kinetic energy
> associated with additional degrees of freedom (motion of the the
> simulation box edge length) added by Parrinello-Rahman barostat is NOT
> subtracted from the kinetic energy of the system when the temperature is
> calculated?
>
> 2) Potential energy also depends on tau_p:
> tau_p Quantity Average
> Err.Est. RMSD Tot-Drift
> 2.0 Potential 374.131
> 120 1535.4 89.344 (kJ/mol)
> 5.0 Potential -1757.13
> 11 225.176 24.8182 (kJ/mol)
> 10.0 Potential -1879.24
> 4.6 186.86 5.23366 (kJ/mol)
> 15.0 Potential -1912.12
> 5.3 183.542 25.0223 (kJ/mol)
> 20.0 Potential -1927.11
> 4.1 198.066 -9.76647 (kJ/mol)
> 25.0 Potential -1922.43
> 7 187.913 -22.8972 (kJ/mol)
> 30.0 Potential -1939.59
> 5.9 175.813 32.3813 (kJ/mol)
> 50.0 Potential -1935.01
> 8.4 182.9 11.7818 (kJ/mol)
> 100.0 Potential -1930.76
> 8.3 199.6 40.4494 (kJ/mol)
>
> I would appreciate if someone can explain the dependence of potential
> energy on “tau_p”.
> Could it be explained by the implementation problem of Parinello-Rahman
> with leap-frog algorithm discussed in the manual: “... using the
> leap-frog algorithm, the pressure at time t is not available until after
> the time step has completed, and so the pressure from the previous step
> must be used, which makes the [Parrinello-Rahman] algorithm not directly
> reversible, and may not be appropriate for high precision thermodynamic
> calculations.”?
>
> Densities and pressures are identical among these simulations. As I can
> see from the density VS time plots the period of density oscillations
> corresponds roughly to 4*tau_p.
>
> Also, it seems that the potential energy goes to plateau when tau_p > 20
> ps. Does it show that for my system I should not use tau_p less than 20 ps
> at given compressibility value and that with tau_p > 20 ps the true NPT
> ensemble is sampled?
>
> Thank you very much.
> Andrey
-----
----
Andrey I. Frolov, PhD
Junior researcher
Institute of Solution Chemistry
Russian Academy of Sciences
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