Hi Sebastian,
> 1.) Given a trajectory file (with say 100 frames), the Sander script
> takes each of these 100 frames as initial structures for short MD
> runs, say 40fs.
> 2.) It determines some order parameter (e.g. a torsion angle), maybe
> also determines an average, and outputs the data into a separate
> external file.
You could do this with a simple shell script.
Start by creating a file called mdin to do the MD run that you want.
Then also write a ptraj.in file
trajin foo.mdcrd
trajout foo.rst restart
Then you run ptraj and it will generate a series of sequentially numbered
restart files for each structure in the mdin file. Also create a ptraj file
for doing the analysis you want in section 2 (e.g. expects a file called
xxx.mdcrd)
You then have something like:
foreach i ( *.rst.* )
echo $i
$AMBERHOME/exe/sander -O -i mdin -p prmtop -c $i -o $i.mdout -r &i.rst -x
&i.mdcrd
mv $i.mdcrd xxx.mdcrd
ptraj prmtop < analyze_mdcrd.trajin > xxx.trajout
mv xxx.trajout $i.trajout
mv xxx.mdcrd $i.mdcrd
#also move any tables produced by ptraj. E.g.
mv order_param.dat $i.order_param
end
and there you have it - quick and easy and with a significant amount of
flexibility since you are running within a standard shell environment. Hence
you could include other things like perhaps a grep to extract a specific
result and append it to a single summary file etc.
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jun 08 2008 - 06:08:11 PDT
