From: cong chen (namd_chcwaaa_at_yahoo.com.cn)
Date: Mon May 18 2009 - 06:11:48 CDT
Dear NAMD users,
I am reading ug for the latest version. When I read about "limitdist", I am quite confused. In the description section, it writes: "the electrostatic and van der Waals potential functions diverge as the distance between two atoms approaches zero. The potential for atoms closer than limitdist is instead treated as ar^2+c with parameters chosen to match the force and potential at limitdist." I noticed that the default value for limitdist is zero. So, if the distance between two atoms approaches zero, how are the electrostatic and van der Waals potential energies calculated giving that limitdist remains the default value?
I would appreciate it if anyone could give me some advice.
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