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

From: Veronika Jurásková <>
Date: Wed, 24 Jan 2018 11:45:23 +0100 (CET)

Dear David,

thank you for the reply. You are right. Since I used organic solvent, all my
system was seen probably as a solute. I changed natcap in prompt file to the
number of last atom before solvent and now it works perfectly.

---------- Původní e-mail ----------
Od: David A Case <>
Komu: AMBER Mailing List <>
Datum: 23. 1. 2018 21:39:19
Předmět: Re: [AMBER] Non-PBC simulation in a droplet made of organic solvent

"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
> minimized it and heated it to 298 K. Then, I run NVT simulation (only MM
> 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
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
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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