[AMBER] Born Mayer Potential

From: Vivien Ramothe <ramothe.vivien.gmail.com>
Date: Tue, 12 Jul 2016 17:36:22 +0200

I'm a PHD student since a couple of month, and i have some troubles using
since it doesn't work for performing NVT simulation on molecules that have
a virtual site.
I'd like to perform molecular dynamics with AMBER i don't have the license
In order to know if it will be useful form me to take a license i need to
know if
there is a way to use the parameters i have for the atoms i use.
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.
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
Could you tell me please if it is possible to implement my own kind of
Does the parmed command work on every steps on the trajectory?
How are the long range correction calculated on a potential that AMBER
doesn't konw?
And if Amber encountered the same kind of problems than CP2K with virtual
Thank you
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Received on Tue Jul 12 2016 - 09:00:02 PDT
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