[gmx-users] Vritual Sites and simulation time-step

Mark Abraham mark.j.abraham at gmail.com
Sun Jun 2 20:16:31 CEST 2013

On Sun, Jun 2, 2013 at 4:56 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> Mark,
> could you also provide me with some examples when usage of VS could give
> artifacts in simulations ?

I don't know of any particular examples. This kind of thing tends to be
tested ad hoc - how far can the time step be pushed and still reproduce
some relevant observable? See GROMACS generalized Born paper. There is
certainly some scope for people to investigate and publish such findings.
See, for example, recent publications by Michael Shirts.

In particular I'm interesting in usage of VS on hydrogens with membrane
> proteins.

I really don't know anything there :-) I imagine people often use a
united-atom lipid for a reason.


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