I interpret "strain" as being the difference in energy between the knitted
form and the isolated polymers (how much intramolecular energy penalty they
pay in order to interact with each other). You can't really just do MM on
the knitted form to determine this, because the un-knitted form does not
have zero energy. In your case, getting the average energy of the free
polymers might be difficult - but it's the only way I know to estimate
internal strain.
On Wed, Mar 19, 2014 at 12:14 PM, Jio M <jiomm.yahoo.com> wrote:
> Hi All
>
> I have polymer chains (4 chains) knitted together and done explicit
> solvent simulation. I am interested to know how much each chain has
> strain/energy (may be not even a correct term to use). I can calculate
> single point energy (MM energy; using imin=5) of backbone but would it be
> sufficient (if not satisfactory) to represent such behaviour?
> Also I am not sure if I can just use atoms as there is residue based
> decomposition of energy or is there any other method that can help in such
> analysis.
>
> thanks
> Jiom
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Received on Wed Mar 19 2014 - 10:00:03 PDT
