Hi Amber users,
I am setting up a simulation with multiple peptides in implicit solvent. To
fix the concentration, I am trying to use a flat-bottom harmonic potential
where the flat region will define the box dimensions. What I am not sure of
is:
1. Do I use the NMR restraints R1-R4? In that case, is there a way to get
the potential to continue to be harmonic (and not flatten out) beyond R1
and R4?
2. These NMR restraints are typically defined as distances, whereas I need
them to be positional restraints. Is there a way to achieve positional
restraints with flat-bottom harmonic?
Thanks in advance.
Chitrak.
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Received on Tue Sep 20 2016 - 08:30:05 PDT
