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

[Miguel Caro]

Hi Mark,

Thanks for your answer. I just created an issue and assigned it to you
(I hope that's OK). Could this be a version problem? I am running 4.6.5
but could run a number of other versions as well.

Thanks again,
Miguel

On 2016-07-28 22:43, Mark Abraham wrote:
> 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