extra bonds

From: Lara rajam (lara.4884_at_gmail.com)
Date: Thu Jul 02 2015 - 09:20:59 CDT

Dear NAMD users !

I would like to fix the sugar puckering during the simulation.
how it should be done in NAMD , do i need to use the dihedral or the
improper flag in the extra bonds.

I have read through and got information like

   - dihedral <atom> <atom> <atom> <atom> <k> <ref>
   - dihedral <atom> <atom> <atom> <atom> <k> <n> <ref>
   - improper <atom> <atom> <atom> <atom> <k> <ref>
   - improper <atom> <atom> <atom> <atom> <k> <n> <ref>

my question is K refers to the spring constant , what should be the
value given to it and what does the other flag n refer to .

if more information is given it will improve my understanding !

thank you !

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