On Thu, Dec 07, 2017, Chase Zagorec-Marks wrote:
>
> I have been trying to perform a simulation of an alanine dipeptide
> chain in water using the Amoeba force field, but I have been having
> some difficulties with the minimization step. Specifically, I have been
> trying to use the following input file:
>
> Minimization of Ala dipeptide for Amoeba
In $AMBERHOME/test, there are a number of sample calcualtions using amoeba,
e.g. amoeba_gb1. Be sure those are working, and then check carefully for
differences between your code and those. (An intial, wild, guess, if you don't
see anything else: try putting the amoeba block after the ewald block.)
In addition, note this: Support for the Amoeba force field is really weak
in Amber right now. We have dropped support for the former pmemd.amoeba
code, and the capability in sander is really legacy code that is both very slow
and hardly used anymore. If you are serious about the Amoeba force field,
you should probably be using Tinker or openMM for now.
The "good" news is that AmberTools18 (coming next year) will have an up-to-date
pmemd.gem code that supports the Amoeba force field, along with other
"advanced" potential energy models.
...hope this helps....dac
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Received on Fri Dec 08 2017 - 06:30:05 PST
