Re: extra bonds

From: Lara rajam (
Date: Thu Jul 02 2015 - 12:35:14 CDT

Dear NAMD !

Thank you for the reply , I am using a amber parameter file, and would like
to run the MD using NAMD .
I would like to fix the puckering with the force constant to be 2 kcal/mol.
is it possible to do this .

What i have understood from this is the k and ref one need to give and i
should only use the improper tag.
one more clarification is , the NAMD says the atom record is from 0 and i
am using the amber file there it starts from 1 ., if some one who has
carried out this kind of simulation can give me some explanations it will
be useful to understand more

thanks in advance !

On Thu, Jul 2, 2015 at 10:48 AM, Josh Vermaas <> wrote:

> Hi Lara,
> I think you would benefit from reading up a bit more on the CHARMM force
> field, and what the individual terms mean. The NAMD tutorial has some more
> detailed explanations (
> but basically you will want to use the first specification, since you want
> to keep the sugar at a specific pucker, which can be done with harmonically
> constrained dihedral angles going around the ring (ie. the potential you
> want to add is like k*(phi-ref)^2). The second specification is if you want
> to add another k*(1+cos(n*phi-ref)) potential term. Impropers are "fake"
> dihedrals that do not describe rotation about a bond, and are usually used
> to keep a planar part of the molecule planar.
> The size of k depends on how big of a tolerance you have for deviations
> from the ideal geometry. kT at room temperature is ~0.6 kcal/mol. How much
> deviation are you willing to tolerate when you run your simulation?
> -Josh Vermaas
> On 07/02/2015 09:20 AM, Lara rajam wrote:
> 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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