On Sun, Nov 9, 2014 at 2:20 PM, Sourav Purohit <sour000.gmail.com> wrote:
> Hi all,
> Is it possible to remove negative normal modes during nmode entropy
> calculation using MMPBSA.py by using large value for maxcyc and a small one
> for drms.
The "drms" value is the key here, you just have to make sure that maxcyc
is large enough to minimize to the drms criteria. But yes, this would be
the general approach by which you would get rid of negative/imaginary
frequencies.
> Is there some way to make sure there are no negative frequencies??
>
Mathematically speaking you need to get to a true local minimum. In
practice, this is difficult to do for large biomolecules with such a
complex potential energy function.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Nov 09 2014 - 15:00:03 PST
