AMBER Archive (2006)

Subject: AMBER: coordinate files

From: Ed Pate (pate_at_math.wsu.edu)
Date: Tue Sep 19 2006 - 15:17:26 CDT

Dear Amber community:

I am trying to simulate the motion of a spectroscopic probe bound to a
protein. The protein is very large and I need to simulate the probe
motion for a long period of time. I need many more simulation time
points for the probe than for the protein as a whole. I also only need
the location of just a few atoms from the probe as a function of time
for analysis. I would like to try and save disk space and speed up
trajectory analysis by writing out a separate coordinate file for just
the probe atoms as a function of time. Could someone point me to the
subroutines where the mdcrd file is written and where ntwx and the other
output control parameters are checked? Are there any other problems I
should be thinking about?

Thanks for the help.

Ed Pate
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