VMD-L Mailing List

From: Paul Grayson (pgrayson_at_ks.uiuc.edu)
Date: Wed May 29 2002 - 11:03:40 CDT

You have three questions:

1: Why would you align something before measuring an RMSD?

We usually align proteins as well as possible before measuring their
differences, because we are interested in their conformational changes
and want to ignore any differences in orientation or position. The
"measure fit" command doesn't align the molecules, but you can align
them the way it's done in print_rmsd_through_time.

2: Why would you weight different atoms differently?

You might consider the motion of heavy atoms to be more significant
than the motion of hydrogen, for example.

3: How should I measure the rate of water diffusion?

Don't worry about weights, since all water molecules should be
weighted equally. Since you don't care about orientation, you can
just use the positions of the oxygen atoms. Don't do any alignment,
since in this case you are interested in changes in position.

Remember that the VMD manual is not going to tell you what to measure.
You need to decide that for yourself; then you can use the commands we
provide if they apply, or, if you want to do something different,
write your own scripts to do the exact calculations that you want.

-Paul