Re: [AMBER] Potential on each atom

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 6 Jul 2016 10:38:05 -0400

On Wed, Jul 6, 2016 at 10:17 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:

> Hi all and Jason,
>
> I need the external electrostatic potential acting on a subset of atoms
> from PME. Is it clearer this way?
>

‚ÄčNot exactly... I don't believe there's any way to have Amber print out
the ESP directly, but I think you can compute it by running a couple
calculations:

1. Compute the PME energy
2. Change the charge of that atom to 0 and compute the PME energy again

The difference between these two calculations divided by that atom's charge
should be the electrostatic potential, I believe (you just have to make
sure to work out the units appropriately). But that value has units J/C.
Note that ParmEd can do a lot of this stuff pretty easily:

energy cut 8
change charge <mask> 0.0
energy cut 8

You'll have to process the output to extract the energy values.

However, this only gives you the pure-MM ESP. If you want the ESP that
takes the electron distribution determined by the QM calculation into
account, it's going to be much harder (and it will be a challenge to get
Amber to do it for you).

Hopefully someone will correct me if I've made a glaring mistake here.

HTH,
Jason

-- 
Jason M. Swails
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Received on Wed Jul 06 2016 - 08:00:02 PDT
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