Nose-Hoover vs v-rescale, low density of the system

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1

GROMACS version: :-) GROMACS - gmx mdrun, 2020.5 (double precision) (-:
GROMACS modification: Yes/No

Hello Everyone,

I have a small cage system (51 atoms) in chloroform solvent, total 2046 atoms. I did NPT equilibriation using T = 298 K, P = 1bar, Thermostat = V-rescale, Barostat = Berendsen. which showed the desired temperature, pressure and density is well equilibriated.

MD run 1: I ran a MD simulation using Thermostat = Nose-Hoover, Barostat = Parrinello-Rahman for 20 ns. The average values of the temperature and pressure were as expected. But the density droped to an averge value of 1217.11 kg/m^3, which is much lower than the liquid choloroform density 1477.75 kg/m^3 at 298 K. Then I have checked the temperature plot against the time of the MD which shows the values are fluctuating a lot.

MD run 2: I changed the thermostat = v-rescale ( and kept Barostat = Parrinello-Rahman as previous) for another MD production run. The average value of density is 1424.7 kg/m^3, which seem to be more acceptable than the previous run.

I found in many discussions that Nose-Hoover is good for big systems, for small systems the flucuations are high, resulting the low density.

My queries are,

  1. Is this combination [Thermostat = v-rescale and Barostat = Parrinello-Rahman] is good enough for MD run?
  2. Do we have any rule to determine which thermostat or barostat will work better for a perticular system? What things should I keep in mind while using thermostat or barostat?
  3. How much difference in the density (compared to the solvent exact density) and/or fuctuations in the temperature or pressure during the production run of equilibriaion is acceptable?
  4. How many atoms are considered as small (or big) system here? I did only QM before, and the cage system seem to be big to me.

Please write about your opinions and suggestions.
Thank you for reading.
Regards
Ranajit

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I am also particularly interested in an answer to your second question. Is there anyone that can elaborate?

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Hello @stan ,

I did not recieved any comments or suggestions. I am sharing my experieneces,

I have used Noose-Hoover, for a system with ~220,000 atoms where they worked properly. But in anouther small system with ~1700 atoms the density was doing very down and pressure was very low so we moved to V-rescale where we saw good equilibriated density and pressure (~1 atm).

Hope this helps.

Regards
Ranajit

1 Like
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What values of tau_t and tau_p did you use?
With NH and PR tau should not be too small and tau_p should be larger than tau_t.

Our general advise it to use:
v-rescale with tau_t=1 ps
c-rescale with tau_p=5 ps