[AMBER] Generating a dimer starting from monomers using MD

From: jacob wick <jacobwick.la.gmail.com>
Date: Thu, 5 Oct 2017 14:56:48 +0530


I am trying to mimic inter H-bonds formed in p-nitrophenol dimer.
I drew two p-nitrophenol molecules and placed them 4Å away from each other
in a chloroform box (I have tried many solvent systems) and my expected
output is a structure showing two inter h-bonds between these two molecules
(attached image). However, after running 100-200ns simulations by keeping
them 4Å away ( I have scanned 4Å- 7Å range in different sets) and also in
different orientations with respect to each other, I am still unable to
obtain a system showing h-bonds as shown below.
I have followed minimization (8000 steps), heating (20ps), equilibration
(2ns) followed by production (100-200ns, room temperature).

Is there any possible way to mimic the interactions between
two p-nitropheno molecules? It's a natural process so I believe it should
be generated using MD protocols stating from two monomers.


[image: Inline image 1]

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Received on Thu Oct 05 2017 - 02:30:04 PDT
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