harmonic distance restraint

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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