Yeah, I think based on some initial MDs I did with larger protein-protein interfaces there is an oscilatory aspect to most, like large bodies tied together with longerchains, where water moves in and out especially around edges, but woundered if it was protein specific or a global phenomina. Just MDs without any pull forces, NPT equed for a while, then allowed to run for extensive periods of time.
Stephan Watkins -------- Original-Nachricht -------- > Datum: Thu, 06 Sep 2012 16:01:26 +1000 > Von: Mark Abraham <[email protected]> > An: Discussion list for GROMACS users <[email protected]> > Betreff: Re: [gmx-users] Calculating number of water molecules involves > between dimer protein. > On 6/09/2012 3:56 PM, Rajiv Gandhi wrote: > > I want to calculate the time dependence of the average number > > of interfacial water molecules in dimer protein ( example hemoglobin), > > > > In experimental results proposed that the water molecules get > > increase/decrease on time scale manner. Is't possible to show up this > > process in MD simulation studies. > > Sure. You just need to come up with a geometric definition for > interfacial and see what happens over a trajectory. > > 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
