pair interaction analysis of multiple trajectories with different timestep

From: Shirley Li (li19104_at_yahoo.com)
Date: Wed May 17 2006 - 10:18:03 CDT

Dear NAMD experts,
 
 1) I have some questions about pair interaction calculations. I have several trajectories, in which different "timestep" (either 1fs or 2fs) was used. I wonder how to do the "Pair Interaction" calculation in one SINGLE run. I saw sb else posted a similar question: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3107.html, while from the answer, the example file only specifies "timestep" =1, and "incr ts 1000". I wonder should "timestep" be specified individually for each trajectory, as well as "incr ts".
 
 2) Besides, for the pair interaction energy between ASP and ARG residues, could anyone give me a rough idea how much is should be?
 
 Thanks a lot.
 
 Shirley
 
                
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