[gmx-users] The md-vv integrator and the choice of cutoffs

[Miguel Caro]

Hi all,

I am simulating a mixture of water and acetonitrile with the OPLS force
field. I am using the md-vv integrator because I want my velocities to
be in synchrony with my positions (md outputs velocities and positions
half a time step apart).

My box is relatively small, 2400 atoms, and I am using 1.3 nm for all
cutoffs. The properties of the mixture evolve smoothly with composition
until the point where I reach the pure acetonitrile extreme, which also
corresponds to the largest box size in the series. L increases with
acetonitrile mole fraction from about 2.86 nm for pure water to 3.39 nm
for pure acetonitrile (T = 323K). For pure acetonitrile the smooth trend
breaks down abruptly and I can observe a severe kinetic energy transfer
from the translational degrees of freedom to the vibrational degrees of
freedom. However, if I increase the cutoff to 1.6 nm the issue goes away.

Also, if I use md as integrator instead of md-vv, with the original set
of cutoffs at 1.3 nm, the issue also goes away. I would like to
understand how/why/whether the choice of integrator and the box size
affect the effect of the cutoffs on the distribution of kinetic energy
in the system. I've gone as far as pinpointing the possible origin of
the issue and a workable solution (i.e. just switch to md), but I would
like to understand the underlying cause of the problem.

Many thanks,
Miguel
-- 
*Dr. Miguel Caro*
/Postdoctoral researcher/
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: *mcaroba at gmail.com*
Work: *miguel.caro at aalto.fi*
Website: http://mcaroba.dyndns.org