VMD-L Mailing List

From: Dominik Bottländer (bottlaen_at_rhrk.uni-kl.de)
Date: Sat Sep 06 2014 - 01:36:43 CDT

Dear Axel, Dear John, Dear Eddi,

Thank you so much for your quick reply to my request and
the helpful information you provided!

@ Eduard Schreiner: You advised me of the true reason for
the missing physical time information in VMD by confirming
my assumption that the DCD file format does not contain
the physical instants of time of the simulation.

@ Axel Kohlmeyer: I actually wrote my own tcl-script to
calculate the RMSD at the different frames of the
respective trajectory to get some experience with
tcl-programming in VMD and to specifically implement the
position based RMSD definition in accordance with the
GROMACS tool "gmx rms"
(ftp://ftp.gromacs.org/pub/manual/manual-5.0.1.pdf#section.8.9).

@ John Stone: Is "physical_time" a prescribed additional
keyword of the "molinfo"-command
(http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ug/node125.html)
referring to the physical time field or is it possible to
specify additional keywords of arbitrary names for the
"molinfo"-command in order to store the physical time
field or other data?

Thank you very much for your answers in advance!

With kind regards,

Dominik Bottländer