Re: [AMBER] Born Mayer Potential

From: David A Case <>
Date: Tue, 12 Jul 2016 21:37:30 -0400

On Tue, Jul 12, 2016, Vivien Ramothe wrote:

> The parameters that have been calculated for dispersion potential are made
> to be
> used with the Born Mayer potential: V(r)=f6*(C6/r6)+f8/(C8/r8),
> the f6 and f8 function are Tang Toennis damping functions.
> I'm reading the user manual since quite a few days now,
> even if if didn't see anything about this kind of potential in it.

That is correct: this sort of function is not implemented.

> It seems i found a way to implement it myself by using the minimize option,
> of parmed command. but i'm not sure about it since i never used it one my
> own.

You would not do this with parmed, but would need to modify the source
code in sander or pmemd. There *is* support for for 12-6-4 potential, so you
could probably use that as a template to construct a 6-8 potential.

> Could you tell me please if it is possible to implement my own kind of
> potential?

It's certainly *possible*, but you would have to be willing to do programming
yourself. OpenMM might be a better option here, since you can define new
types of potentials at a fairly high (Python) level.

> How are the long range correction calculated on a potential that AMBER
> doesn't konw?

Amber has long-range corrections for dispersion (an r^-6 potential), and you
can use that as a template to implement something similar for a 6-8 function.
Again, programming is required. (Not sure what OpenMM can do in this regard.)

> And if Amber encountered the same kind of problems than CP2K with virtual
> site?

Amber supports a limited number of types of virtual sites, so you should study
that section of the manual to see if it meets your needs. I have no idea
what problems CP2K has--generally, one would not think of Amber as any kind
of replacement for CP2K, but I am not familiar with all the capabilities of
the latter.


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Received on Tue Jul 12 2016 - 19:00:02 PDT
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