On Fri, May 29, 2020, Pinky Mazumder wrote:
>
>I can place the chains parallel to each other. After that, I need to see
>the h-bond interaction between the polymers. For that I ran the simulations
>with energy minimization, heating and production MD.
>
>Even after, I do not see the H-Bond. To do so, what process I need to
>follow?
I guessing you need a better starting structure. Do the chains move
much during the simulation? If there are no inter-chain hydrogen bonds
in the starting structure, it may difficult to get them to form just
with MD, even if the H-bonded structure has a lower free energy.
You may be able to get some good ideas, plus a feeling for how mobile
your chains are, by looking at the trajectories you have. Generally, MD
simluations sample configurations close to the starting point, and
either long simulations or advanced sampling methods are required to
find quite different structures.
If you know what H-bonds you would like to form, you could add
restraints (called "NMR" restraints in Amber lingo, for historical
reasons) that will pull the H-bond donor and acceptor atoms to an
H-bonding geometry.
....good luck...dac
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Received on Fri May 29 2020 - 10:00:02 PDT
