Dear Carlos
That was nice suggestion indeed.
thinking over this, can we see this like in othrewise way: If I consider a polymer chain and do MM energy on each resdiue the polymer made of it can give me hot spot where I have most strain along the chain length.
On Wednesday, March 19, 2014 4:43 PM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
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 - 10:30:03 PDT
