On Thu, Nov 12, 2015 at 11:56 AM, Balaji Selvam <bselvam01.gmail.com> wrote:
> Dear Amber Users,
>
> I would like to simulated infinite DNA molecule.
>
> I came across similar posts in archives (
> http://archive.ambermd.org/200507/0107.html) although its very old post.
>
The information here is actually still accurate. Amber does not permit
bonds to cross periodic boundaries, so infinite DNA systems are impossible
in Amber right now.
They will also be very difficult (if not impossible) to correctly build in
tleap, seeing as Amber has never supported PBC-spanning bonds. I know
other packages allow bonds crossing periodic boundaries, but the only one
I'm sure that does it is GROMACS.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 12 2015 - 10:30:02 PST
