From: X Zheng (zheng042003_at_yahoo.com)
Date: Tue Jan 16 2007 - 16:02:59 CST
Dear NAMD expert,
I have two questions about harmonic restraint to be applied two a pair of two atoms. I saw the relevant message at http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4984.html and the response from Luca.
1) One of my question is, if i need to change the force constant in ONE configuration file, is the followiing syntax correct?
###############
tclforces on
firsttimestep 500000
tclforcesScript file2
run 200000
firsttimestep 500000
tclforcesScript file2
run 200000
firsttimestep 500000
tclforcesScript file3
run 200000
firsttimestep 500000
tclforcesScript file4
run 200000
####################
where the force constant is reduced gradually in file1, file2, file3, and file4. Since the output .log file doesn't report much information about the input from file tclforcesScript, I'm not sure weather the restraint I need is applied or not. Could sb provide any further info.?
2) Regarding the force constant, I saw some people suggest 100, others suggest 5. In my .conf file part of which are shown above, I start with 50, then reduce it to 48, 46, 44, ..., 2, 0, reducing 2 a time, with each one running for 200 ps with 2fs of timestep. Are these settings acceptable?
Any help and info will be greatly appreciated.
Shirley
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