Please thanks so much for your support but I still do not get what all you are talking about is....
On 13 May 2013 11:44, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/13/13 1:48 AM, Acoot Brett wrote: > >> Dear All, >> >> Will you please explain how the initial velocity may affect the MD >> results? >> > > We use different initial velocities to improve sampling, i.e. to allow the > trajectory to evolve in different ways. In the end, in the limit of > infinite sampling, the trajectory ensemble averages should be the same. > > > What the initial velocity really means? >> > > Just what it claims to be - the initial (first) velocities of each atom. > > > How the velocity of the atoms in the protein changes in the MD process? >> > > Please read about MD integration algorithms. > > > What is the reasonable scope of the initial velocity? >> > > I don't know what this means. > > > Any suggestions on how to manually input a defined initial velocity? >> > > Provide grompp with an input file that has velocities - .trr, .edr, .gro, > .cpt. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
