[gmx-users] essential dynamics
spoel at xray.bmc.uu.se
Tue Aug 9 08:23:32 CEST 2005
On Mon, 2005-08-08 at 16:45 -0600, Anthony Cruz wrote:
> Hi Users:
> I am interested in perform essential dynamics analysis to my simulation and I
> have some questions.
> For the analysis I will use the part of the trajectory when the rmsd is
> constant or all the trajectory?
Assuming you have an equilibrium trajectory you should use all. If you
only want to study what happens very close to the crystal structure you
could use a subset, but how do you justify that?
> When I do the Posen cosen analysis, I will use the PC's that have the lower
Don't understand the question.
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users