From: Arturas Ziemys (ziemys_at_chbmeng.ohio-state.edu)
Date: Sat May 19 2007 - 10:47:16 CDT
I want to simulate long n-alkanes with NAMD using OPLS-UA FF (Jorgensen, 1984). But I miss something how to put dihedral Fourier parameters into NAMD "style". For OPLS there are optimized 3 dihedral sinusoids, if I'm following right (V = V0 + 1/2V1(1+cos(w)) + 1/2V2(1-cos(2w)) + 1/2V3(1+cos(3w))).
NAMD has for dihedral K (1 + cos( n*(w-d) )). Does it mean that I should put tree sinusoids into NAMD parameter file like :
A B C D K n d K n d K n d
How to adopts Jorgensen dihedral potential to NAMD ? Or, in general, is there any sense to include that dihedral potential into MD of long n-alkanes ?
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