[gmx-users] sd integrator and P-R barostat/ACETONITRILE with CHARMM ff

Sonia Milena Aguilera Segura sonia-milena.aguilera-segura at enscm.fr
Mon Jul 17 18:17:42 CEST 2017

>>> I increased the size of the simulation box to 4 nm. Indeed, the values of
>>> pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However,
>>> the T keeps being overestimated (302 K). During NVT I got the right value,
>>> so I decided to run the 200 ns NPT equilibration with Berendsen barostat
>>> instead of P-R. I got the right T value, around 298.3 and a pressure of
>>> 1.5 more or less. Then I launched a continuation test with 200 ps MD with
>>> P-R (I couldn't use the -e option because it gives me the error Could not
>>> find energy term named 'Box-Vel-XX', moreover, I didn't use P-R before so
>>> I guess I shouldn't expect stored values for it?. But I am using -t ).
>>> Despite I got low pressure averages around 0.5 bar, the temperature raised
>>> again to 301-302. This happens very early in the simulation, which seems
>>> to indicate that for sd integrator/thermostat and P-R barostat there is
>>> something going on. I am getting practically the same density in between
>>> simulation, so I guess I can say t
>>   ha
>>>    t in term of P, the system has been equilibrated. However, what can I do
>>>    to get the right T for this system? If I was able to get the right T
>>>    with Berendsen barostat, I don't understand what's wrong when I change
>>>    to P-R.
>> Sounds buggy.  What version of GROMACS are you using?  There were temperature
>> issues with the Langevin integrator in previous versions, but those should
>> have
>> been long since solved.
>> I am using version 5.1.2. I checked the release notes for version 5.1.3 and 5.1.4 and the only thing related with sd integrator (none) or P-R barostat is this one 'Fixed Parrinello-Rahman with nstpcouple > 1'. Can this be the cause?

>I don't know.  Upgrade to 2016.3 and try again.


Dear Justin, 

I upgraded to 2016.3 and did several tests. In all cases I ran first a NVT with sd and 200 ps NPT with Berendsen. I always got a T of 297.6-298.6 for equilibrations. Then, for instance,  I ran a 4 nm box with isopropanol, which is bigger than acetonitrile, and got a T of 300 K instead of 302 K, for the same system with the 5.1.2 version. For a 4 nm box of acetonitrile I got also a small improvement: 299.5 vs 300-301 for the previous version. So, I guess there was something wrong with the version. Still, I am wondering if the level of precision is enough (an error of +-1.5 K), considering that I am getting very precise values for Berendsen barostat, even for the 3 nm boxes for both solvents. Also, my average P is -1.5 and 1.5.. which is giving me very similar results for density in all cases. Can I assume that those values are ok (even the negative) considering the expected fluctuations during the MD simulation?

Thank you, 

Best regards, 

Sonia Aguilera 
PhD student

More information about the gromacs.org_gmx-users mailing list