From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu May 02 2013 - 08:17:00 CDT
I'm not so familiar with the formats of force fields other than CHARMM, but I want to convert one for OPLS to CHARMM-style for running in NAMD. The main issue I've yet to resolve though is the format of the dihedrals. Here's an example line from the original parameter file:
; ai aj ak al funct ; Amber type OPLS type Type V1 V2 V3 Comments
1 4 5 6 3 -0.50208 -1.50624 0.00000 2.00832 0.000 0.000 ; C3-N3-C2-C2 4031-4030-4032-4004 5000 0.000 0.000 -0.240
I realize the first part is an RB format. The second part, I guess (please correct me if I'm wrong!!!), uses this functional form:
V(φ) =V1(1+ cosφ)/2+V2(1−cos2φ)/2+V3(1+ cos3φ)/2+V4(1−cos4φ)/2
So for the example line, the potential would be V = -0.12*(1+cos(3*phi)). But how to represent this in CHARMM??? Because it can't be JUST a phase shift, then we would have V = 0.12*(1+cos(3*phi-180)) = 0.12*(1-cos(3*phi)). In other words, there is a constant shift in the potential energy equal to V3.
What simple fact am I misunderstanding here? How does one convert force constants less than zero to charmm, where they are always greater than zero?
Thanks!
JC
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