From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri May 04 2012 - 08:12:26 CDT
On Fri, May 4, 2012 at 8:33 AM, Hall McDull <jerviedog_at_gmail.com> wrote:
> 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
> 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?
yes, if the bond is constrained to be rigid (via SHAKE)
and for that you don't need a force constant but an
> 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
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.
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