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

[Mark Abraham]

Hi,

In principle, there should be no differences, but in practice the care that
has gone into the md integrator exceeds that of md-vv. If you could open an
issue at redmine.gromacs.org, including .tpr and mentioning GROMACS
version, then probably we can work out what the issue is.

Mark

On Thu, Jul 28, 2016 at 9:17 PM Miguel Caro <miguel.caro at aalto.fi> 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
> --
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