# Nose-Hoover vs v-rescale, low density of the system **URL:** \ **Category:** User discussions\ **Created:** [July 25, 2022, 5:00am UTC](https://gromacs.bioexcel.eu/t/nose-hoover-vs-v-rescale-low-density-of-the-system/4507 "2022-07-25T05:00:15Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Tijanar](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/tijanar/32/1498_2.png) [@Tijanar](https://gromacs.bioexcel.eu/u/Tijanar)\ **Post date:** [July 25, 2022, 5:00am UTC](https://gromacs.bioexcel.eu/t/nose-hoover-vs-v-rescale-low-density-of-the-system/4507/1 "2022-07-25T05:00:15Z")
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 ---
**Author:** ![stan](https://avatars.discourse-cdn.com/v4/letter/s/51bf81/32.png) [@stan](https://gromacs.bioexcel.eu/u/stan)\ **Post date:** [April 12, 2023, 1:06pm UTC](https://gromacs.bioexcel.eu/t/nose-hoover-vs-v-rescale-low-density-of-the-system/4507/2 "2023-04-12T13:06:00Z")
I am also particularly interested in an answer to your second question. Is there anyone that can elaborate? ---
**Author:** ![Tijanar](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/tijanar/32/1498_2.png) [@Tijanar](https://gromacs.bioexcel.eu/u/Tijanar)\ **Post date:** [April 26, 2023, 3:42am UTC](https://gromacs.bioexcel.eu/t/nose-hoover-vs-v-rescale-low-density-of-the-system/4507/3 "2023-04-26T03:42:06Z")
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 ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [April 26, 2023, 6:57am UTC](https://gromacs.bioexcel.eu/t/nose-hoover-vs-v-rescale-low-density-of-the-system/4507/4 "2023-04-26T06:57:56Z")
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