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

James Starlight jmsstarlight at gmail.com
Mon Jun 3 14:03:35 CEST 2013


I've performed 50 ns simulation of water-soluble protein with and without
VS. As the consequence I've observed similar behavior of both systems in
case of secondfary structure conservation as well as overal degree of
conformational dynamics. Also I didnt observed any fluctuation in energy
and temperature (using SD as the thermostat and 2ps coupling).  Is there
any other Gromacs build-in tools on what I should paid more attention
during investigation stability of the system with VS ?


2013/6/2 Mark Abraham <mark.j.abraham at gmail.com>

> 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.
> Mark
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