it's not clear what you're asking, but no the NMR distance restraints won't
work (AFAIK) as positional restraints. for R1 and R4 not flattening out,
you can just use very short and very long distances as the place where they
will flatten.
On Tue, Sep 20, 2016 at 11:12 AM, Chitrak Gupta <chgupta.mix.wvu.edu> wrote:
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 20 2016 - 09:00:02 PDT
