On Fri, Feb 12, 2016 at 12:51 PM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
> Did anyone use the 12-6-4 set in NAMD ? Is NAMD able to read the
> additional lines necessary in the AMBER topology files ?
>
I'm pretty sure if you want to use the 12-6-4 potential, you have two
options: Amber and OpenMM. And if you want to run on GPUs, your only
option is OpenMM. ParmEd has an "OpenMM" action that will behave like
sander and pmemd (it will read sander input files and run an equivalent
simulation with OpenMM). If you have a 12-6-4 potential set there, then it
should use that correctly. This is described in the Amber manual.
No other code out there supports this
potential form (at least that I'm aware of).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 12 2016 - 15:00:04 PST
