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.abra...@gmail.com> > On Sun, Jun 2, 2013 at 4:56 PM, James Starlight <jmsstarli...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
