From: Hall McDull (jerviedog_at_gmail.com)
Date: Fri May 04 2012 - 07:33:48 CDT
Dear NAMD users,
Recently I read through the par_all22_sugar.inp file, and I found a record
in the BOND section:
HT OT 450.0 0.9572 ! from TIPS3P geometry
HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE
w/PARAM)
My question is: If the Kb of the bond is zero (the second line above), why
bother to have a record of the this bond in the BONDS section? Does this
has some effect on the simulation?
Moreover, what if the Ktheta of the angle is zero, but I write this angle
out in the ANGLES section? Does this affect the simulation? What about Kchi
in the DIHEDRALS section? For example, I found the line below in the
DIHEDRALS section of the par_all27_prot_na.prm file:
NH2 CT1 C O 0.0000 1 0.00
Thanks for guides or comments.
Best regards,
Jianfeng He
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