# My system blows up in Parrinello-Rahman barostat but not in Berendsen

**URL:** <https://gromacs.bioexcel.eu/t/my-system-blows-up-in-parrinello-rahman-barostat-but-not-in-berendsen/1747>\
**Category:** User discussions\
**Tags:** mdp-parameters\
**Created:** [March 15, 2021, 1:33am UTC](https://gromacs.bioexcel.eu/t/my-system-blows-up-in-parrinello-rahman-barostat-but-not-in-berendsen/1747 "2021-03-15T01:33:51Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![ehsan](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ehsan/32/1345_2.png) [@ehsan](https://gromacs.bioexcel.eu/u/ehsan)\
**Post date:** [March 15, 2021, 1:33am UTC](https://gromacs.bioexcel.eu/t/my-system-blows-up-in-parrinello-rahman-barostat-but-not-in-berendsen/1747/1 "2021-03-15T01:33:51Z")

</div>

GROMACS version: 2020.4  
GROMACS modification: No

Dear all,

I have a small box of chlorobenzene molecules and I’m using OPLS-AA FF and I got the parameters and charges from the LigParGen server. When I run the production MD in NPT, if I use Parrinello-Rahman barostat and Nose-Hoover thermostat the system will blow up. Conversely, If I use the Berendsen barostat and V-rescale thermostat everything is fine.

I tried more restrict energy minimization and equilibration on NVT and NPT with more time (200ps) and also a prior NPT simulation (200ps) without constraint in Berendsen barostat followed by a production NPT in P-R and it always blows up in few steps.

If there is something wrong with my simulation why is it all good in Berendsen? It gives reasonable density and dielectric constant too.

I have attached the mdp and topol files and em.gro (as em.dat) in case you want to take a look at them.

[md\_relaxation\_Berendsen.mdp](https://gromacs.bioexcel.eu/uploads/short-url/ovdAt4M1kmMdAjxBNZCFBWLL0GQ.mdp) (2.7 KB)  
[md\_PR.mdp](https://gromacs.bioexcel.eu/uploads/short-url/1cq31BQiL7Js9LZbBDZnpR4qOPx.mdp) (2.7 KB)  
[topol.top](https://gromacs.bioexcel.eu/uploads/short-url/zMUmvoe2VVsJ7uVyy7CBUQZ68w3.top) (6.1 KB)  
[em.dat](https://gromacs.bioexcel.eu/uploads/short-url/jarmgjQovOfE1U0rEZ1esMYkIq5.dat) (459.9 KB)

---

<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [March 16, 2021, 10:31am UTC](https://gromacs.bioexcel.eu/t/my-system-blows-up-in-parrinello-rahman-barostat-but-not-in-berendsen/1747/2 "2021-03-16T10:31:17Z")

</div>

Hi,  
What about Parrinello-Rahman barostat and V-rescale thermostat? Or you can try also stochastic cell rescaling (as barostat). “The stochastic cell rescaling algorithm is a variant of the Berendsen algorithm that allows correct fluctuations to be sampled.”  
[https://manual.gromacs.org/current/reference-manual/algorithms/molecular-dynamics.html#pressure-coupling](https://manual.gromacs.org/current/reference-manual/algorithms/molecular-dynamics.html#pressure-coupling)

This post may also be of interests

> [@Choice of thermostat during production MD: Nosé-Hoover vs. V-Rescale](https://gromacs.bioexcel.eu/t/choice-of-thermostat-during-production-md-nose-hoover-vs-v-rescale/1420):
>
> GROMACS version: 2020.4 GROMACS modification: No Dear GROMACS User Forum, Is the combination of Nosé-Hoover thermostat / Parrinello-Rahman barostat preferable over the combination of V-Rescale thermostat / Parrinello-Rahman barostat, during production MD? Do you have any suggestions on how I should proceed if my system is stable with V-Rescale / Parrinello-Rahman, but not with Nosé-Hoover / Parrinello-Rahman? Thank you so much for any comments! Happy New Year & Best Regards, Stefan

Best regards  
Alessandra

---

<div class="post-metadata">

**Author:** ![kevinboyd](https://avatars.discourse-cdn.com/v4/letter/k/c77e96/32.png) [@kevinboyd](https://gromacs.bioexcel.eu/u/kevinboyd)\
**Post date:** [March 17, 2021, 3:06pm UTC](https://gromacs.bioexcel.eu/t/my-system-blows-up-in-parrinello-rahman-barostat-but-not-in-berendsen/1747/3 "2021-03-17T15:06:21Z")

</div>

Also, 200 ps really isn’t a ton of equilibration time, if there’s something unstable about your starting configuration. It’s probably worth trying 10s of nanoseconds of Berendsen to see if your system stabilizes after that - should be very feasible with a small box.