(no subject)

From: Andrew Aird <a.aird_at_physik.uni-stuttgart.de>
Date: Wed 31 Jan 2001 20:46:10 +0100

Dear Amber users

I'm having difficulties, calculating the RMS with ptraj.
My protein is a trimer which consists of 3 parts that are not allowed to move
and 3 parts that are allowed to move freely. When I claculate the RMS for the
whole trimer (all atoms) I get RMS values around 40A .
The next thing I did was calculate the RMS for each of the moving parts
seperately, by using the mask option in the ptraj input file. But the result is
not what I would expect. Since I'm not considering the fixed part, I would
expect a RMS that schould be larger than for the whole trimer. But
this isn't the fact at all. The RMS is much smaller...

My question is:

How does ptraj calculate the RMS ??? (Does the mask option do anything
special other than chose the atoms for which ptraj calculates the RMS? I
wouldn't think so.)

(Well, I allways thought I knew how a RMS is calculated...)


Thanks in advance

Andrew





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Andrew Aird
3.Physikalisches Institut
Universitšt Stuttgart
Pfaffenwaldring 57
D 70569 Stuttgart
e-mail: a.aird_at_physik.uni-stuttgart.de
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Received on Wed Jan 31 2001 - 11:46:10 PST
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