Re: [AMBER] Non-PBC simulation in a droplet made of organic solvent

From: David A Case <>
Date: Tue, 23 Jan 2018 15:38:12 -0500

On Mon, Jan 22, 2018, Veronika Jurásková wrote:
> I am trying to run QM/MM simulation of small organic molecule in organic
> solvent (THF) using electronic embedding. I would like to use non-PBC
> simulation in a droplet. I prepared the system (organic molecule + 999 THF),
> minimized it and heated it to 298 K. Then, I run NVT simulation (only MM in
> Amber) to let the system relax for 100 ps before the QM/MM simulation.
> Because the droplet in a vacuum is a little unphysical, I tried to use
> solvent cap to avoid evaporation into vacuum.
> When I checked the trajectory in VMD, there were some THF molecules
> evaporating from the sphere.

You need to be sure that the cap force is being applied to all the THF
molecules. Are you seeing a RESTRAINT energy in the mdout file: cap penalties
show up as restraint energies.

I suspect that the value of "natcap" in your prmtop file might be incorrect:
the manual says that the cap function refers to a "water cap", and it might not
be getting set up correctly for non-water solvents.

Look in your prmtop file for the CAP_INFO section: what is the first integer
there? Does it correspond to the atom number of the first THF molecule?


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Received on Tue Jan 23 2018 - 13:00:01 PST
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