Subject: SUMMARY:CHARMM Trajectory Analysis

From: "Xiang(Simon) Wang" <[email-masked]>
Date: Sun, 23 Sep 2001 15:29:14 -0400 (EDT)

Dear CCLers:

Thanks for all the replys to my question about CHARMM trajectory analysis. 
The atomic average RMSD is just located at the weighting array of the
average coordinates. It is embarrassing that I didn't even know where the
weighting array is at the begining and didn't realize the RMSD is in the
average coordinates already. Two websites are good for CHARMM users:

http://www.psc.edu/general/software/packages/charmm/tutorial/index.html
http://www.ch.embnet.org/MD_tutorial/

Following are the summaries of the answers. Thanks again.
------------------------------------------------------------------------
Rick Venable

I've appended a script I've used to get the RMSD about the average
structure for CA atoms in a protein, and write a .crd file with CA atoms
only.  The RMSD data is in WMAIN, the last column of real numbers in a
.crd file; you can extract the data for plotting vs. the RESID via e.g.

grep ' CA ' file.crd | awk '{print $2, $10} > ca-rmsd.dat

* NPgT aquaporin 1fgy tetramer; check protein CA movement 
*

stream init-p21.str  ! READ RTF/PARAM/PSF/COOR
coor copy comp       ! REQUIRED FOR ORIENT IN COOR DYNA

! OPEN TRAJECTORY FILES
set j 1
set u 21
label tlp
open unit @U file read name [email-masked]
incr u by 1
incr j by 1
if j .le. @N goto tlp

! COMPUTE AVERAGE AND RMSD AFTER ALIGNMENT WITH INITIAL COORDS
coor dyna firstu 21 nskip 1000 nunit @N -
  sele atom % * CA end orient sele atom % * CA end

! WRITE THE CA ATOMS TO A FILE
open unit 10 write card name avgcat1.crd
write coor card unit 10 sele type CA end
* average ca coords, with isotropic fluctuations in wmain
*

stop

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Tru Huynh

Checkout this fine tutorial:

http://www.ch.embnet.org/MD_tutorial/index.html
section III
Analysis of a MD simulation
section IV
CHARMM exercise 1 ....
http://www.ch.embnet.org/MD_tutorial/pages/CHARMM.Exercise1.html
and the input file:
http://www.ch.embnet.org/MD_tutorial/Exercises/exercise1a/input/md_anal.inp

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