pair.pdb and cutoff for pairInteraction

From: Shirley Li (
Date: Tue Nov 29 2005 - 11:00:02 CST

Dear NAMD expert,
 I have some questions about pairInteraction.
 I need to know the interaction between two groups (I and J) of atoms throughout the MD trajectory. I read some threads from the NAMD-list, while I still have some Qs as follows:
 1) For the pair.pdb file, I'm not clear about the "B column". Could sb give me a sample pair.pdb file?
 2) Is there any way to set a distance cutoff, so that any atom in one group falls beyond the cutoff from the other group will be ignored for consideration of the calculation?
 3) To execute the calculation, should I prepare a conf file as usual, and submit the NAMD job?
 Your help will be greatly appreciated.
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