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 <[email protected]> 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 <[email protected]> > >> On Sun, Jun 2, 2013 at 4:56 PM, James Starlight <[email protected] >>> 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 >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
