On 2/09/2012 1:04 AM, Bala subramanian wrote:
Hi justin,
Thanks and sorry for the delayed response.
I understand from the link that g_msd choose multiple restarts in a
given traj and averages the msd from the restart point to the end of
the trajectory. I would like to know if i can avoid such restart
points. I would like to choose one starting point as the reference and
calculate the msd of each succeeding points with respect to the
starting.
OK, so have a read of g_msd -h and choose what you want to do.
Mark
Thanks
Bala
On Wed, Aug 22, 2012 at 6:16 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 8/22/12 12:12 PM, Bala subramanian wrote:
Hi justin,
Thanks for the suggestion. I will look at the code. Meanwhile I have
one doubt regarding the following option of the g_msd tool.
“-trestart time 10 Time between restarting points in trajectory
(ps)”
What does this -trestart indicates actually. I did a small trail run
on a 100ps trajectory (containing 500 snapshots) with snapshots
collected at .2ps interval. In the output file, it is printed as “#
MSD gathered over 100 ps with 11 restarts”.
Does it mean that the MSD is calculated with 11 different reference
coordinates.
http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html
-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
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