Some basic questions about NAMD

From: Shirley Li (li19104_at_yahoo.com)
Date: Tue May 09 2006 - 15:01:37 CDT

Dear NAMD experts,
 
 I have some basic questions about NAMD as follows:
 
 1) In the configuration parameter file, if I have water box size of 10 ang. thick ("-t 10" when using "solvate") , should "cutoff" be GREATER than 10? This way, in case any part of the protein moves away from the center box, its image is still within the range of non-bond interaction cutoff.
  
 2) During the simulation, does NAMD by default do any recentering of the whole system or the protein every certain steps?
  
 3) Is there any way to computer the min and max distances between the protein and its image?
 
 Any information/suggestion will be very much appreciated.
 
 Shirley
 
                
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