Re: [AMBER] Generating a dimer starting from monomers using MD

From: Karl Kirschner <>
Date: Thu, 5 Oct 2017 12:57:46 +0200

Hi Jac,

  A couple of suggestions. Have you tried to see if you can obtain a stable
dimer using just molecular mechanics minimization (i.e. no MD, no chloroform)?
This would tell you something about the force field, and if it were
possible at all. Second for you MD simulation, I think it will very much
depend on the temperature that you run the simulation. Maybe room
temperature is too high to observe long-lived dimer formation. Try some
temperatures that a lower until you observe what you think you should. (Too
low of a temperature will result in not enough molecular motion to sample
configurational space. Too high of a temperature would result in high
kinetic energy/motion of the molecules.)


On Thu, Oct 5, 2017 at 11:26 AM, jacob wick <> wrote:

> Hi,
> 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.
> Thanks,
> Jac
> [image: Inline image 1]
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Received on Thu Oct 05 2017 - 04:00:01 PDT
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