Re: [AMBER] Apply Lennar-Jones potential between small molecules

From: Ming Tang <>
Date: Thu, 18 Mar 2021 04:15:18 +0000

Dear Carlos and David,

Thank you very much for your guidance. Yes, I found that a positive rk2 does the right thing and the problem lies in how the system calculates the distance between two IGRs. I found out that the system calculates the distance based on the coordinate before autoimage, and therefore the small molecules do not get close in the trajectory before the autoimage process. I guess this comes from the periodic boundary condition setting.

Is there a way to fix this?

Many thanks,
From: Carlos Simmerling <>
Sent: Tuesday, 16 March 2021 11:41 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules

On Tue, Mar 16, 2021 at 8:56 AM David A Case <> wrote:

> On Tue, Mar 16, 2021, Carlos Simmerling wrote:
> >yes negative rk gives an inverted parabola, so it is repulsive if it is
> >outside the flat region.
> I'm a little confused here, and would recommend careful testing if you are
> setting rk2 to a negative number. I've not done that but it *sounds*
> dangerous. Probably a good idea to numerically plot the function vs.
> distance, and make sure you are getting the behavior you want.
Dave is right, this can be really dangerous since it goes to infinitely
negative energies. I've used it and technically it does work, but it's
probably much safer to use other options. I should have been more careful
in giving caution along with my reply!

re-reading the original question, a negative rk2 will make them ATTRACTIVE
below r2, and it doesn't sound like this is what you want. *For repulsive
interaction below r2 you want a positive rk2.*
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Received on Wed Mar 17 2021 - 21:30:02 PDT
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