[gmx-users] Problem with Gromacs and Charmm force field dump rates

Vivien WALTER walter.vivien at gmail.com
Thu Feb 8 12:28:11 CET 2018

Dear all,

We are experiencing a strange problem with all-atom simulations using
Gromacs and Charmm force field, and we have trouble to sort it out.

We are simulating a single-ring sugar and we observe radically different
behaviors of the molecule as a function of the simulation dump rate.
Starting from the same .gro file with continuation = yes (so using the same
initial velocities written in the file), the interactions of the sugar with
its surroundings is different between two simulations if the following set
of parameters are changed: nstxout, nstvout, nstenergy and nstlog. Between
the two .mdp files, absolutely no other parameters are changed. As an
example of what differs between the simulation, the box size along X and Y
axis are increasing with low dump rates (2500 steps) but decreases with
high dump rates (25000 steps).

We tried to reproduce the problem with a box filled with only water
molecules, but in this configuration there is no difference between our
results when different dump rates are used. Following the previous example,
the evolutions of the box size superimpose perfectly for different dump
We tried to change the conformation of the sugar to see if it would have an
impact on the problem observed, but the problem remains.

The forcefield used is Charmm36 (version from june 2015) and Gromacs
version is 2016.4. For the sugar, the structure file was constructed
according to the more stable chair conformation of the saccharide, but the
force field of the molecule was directly taken from the standard Charmm
force field parameters. Water model used is TIP3P.
For the simulation parameters, the pressure coupling used is a
semi-isotropic Parrinello-Rahman set at 1.0 bar in both directions
(compressibility 4.5e-5 and tau_p equals to 2.0). For the temperature
coupling, we used first V-Rescale, but as we suspected the stochastic
process to lead to different results for different dump rates, we also
tried a Nose-Hoover thermostat. In both cases, the three molecular groups
are coupled separately at the same temperature and the same tau_t (0.4)
The rest of the main options for the .mdp file are taken from the
recommanded parameters for using Charmm36 in Gromacs (
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM )

Is it a known problem of Gromacs using Charmm36? Is there a way to fix the
problem and obtain identical results, or at least similar evolutions?

Thanks you in advance for your help,
Best regards,

Dr. Vivien WALTER
Institut Charles Sadron
23, Rue du Loess
BP 84047
67034 STRASBOURG CEDEX 2, France
tel: +33(0)388 414 113
fax: +33(0)388 414 099

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