AMBER Archive (2009)

Subject: Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Sat Oct 31 2009 - 09:59:14 CDT

2009/10/31 Tom Joseph <ttjoseph_at_gmail.com>:
> According to the documentation it's not NTYPES x NTYPES, it is
> NTYPES*(NTYPES+1)/2), which you can verify by looking at a valid
> prmtop file.

To be clear, I was referring to the LENNARD_JONES_ACOEF,
LENNARD_JONES_BCOEF, etc blocks. The NONBONDED_PARM_INDEX, which
indexes these arrays, is indeed NTYPES x NTYPES in length.

--Tom

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