- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

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?
*

*>
*

Not 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

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:

Not 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Jul 06 2016 - 08:00:02 PDT

Custom Search