[gmx-users] ACETONITRILE with CHARM ff

Justin Lemkul jalemkul at vt.edu
Thu Jul 13 14:58:18 CEST 2017

On 7/12/17 8:56 AM, Sonia Milena Aguilera Segura wrote:
>> Message: 3
>> Date: Tue, 11 Jul 2017 12:57:05 -0400
>> From: Justin Lemkul <jalemkul at vt.edu>
>>> Moreover, I observed that this time I got lower values for P during the NPT
>>> equilibration, but still is too far from 1 bar.  I really don't understand
>>> why for the NVT simulation I get a T around 298, but as soon as I turn on
>>> the pcoupl, the T rises to 300-301 K and the P gets average values of 7
>>> and 4 bar (vs 8 and 14 for the previous simulations). Then at the end of
>>> the 1-ns MD the temperature remains around 301 and the P is -1 and 2.7
>>> bar. Considering the parameters I am using, is there anything I can change
>>> to make the P coupling better? I am running a 3 nm box with 308 molecules.
>>> This is the full mdp file:
>> http://www.gromacs.org/Documentation/Terminology/Pressure
>> Your box is very small and will be subject to large fluctuations.
> Dear Justin,
> 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 tha
>   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.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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