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

[Erik Marklund]

Hi James,

Not related to the integration stability as such, but since the vsites affect the hydrogens by definition perhaps g_hbond can reveal systematic differences between simulations with and without vsites. I believe Feenstra et al did this in the paper describing vsites in the first place.

Erik

On 3 Jun 2013, at 14:03, James Starlight <jmsstarlight at gmail.com> wrote:

> Mark,
> 
> 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 ?
> 
> 
> James
> 
> 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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