From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Jul 03 2015 - 09:08:25 CDT
Then you've misunderstood it. Don't use impropers. This isn't an
improper that you are restraining, but instead the 6 dihedral angles
that contribute to the pucker.
On 07/02/2015 12:35 PM, Lara rajam wrote:
> 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
> 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 <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>> 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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