Hi Karl,
I have tried to analyse the results of molecular mechanics minimization,
but it was not showing me the desired output. Trying different orientations
of the monomers are giving different minimized states, trapping in local
minima (with only one inter H-bond) was also observed. I have already
performed temperature scan but it was not successful.
Thanks for you suggestions!
Regards,
Jac
On Thu, Oct 5, 2017 at 4:27 PM, Karl Kirschner <k.n.kirschner.gmail.com>
wrote:
> 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.)
>
> Bests,
> Karl
>
> On Thu, Oct 5, 2017 at 11:26 AM, jacob wick <jacobwick.la.gmail.com>
> 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 - 06:00:09 PDT
