Hi, Chitrak
There is the way to customize collective variable in NFE module, and the
example I gave in the tutorial in just the projection of distance,
you can learn from here.
http://kili.physics.ncsu.edu/~feng/AmberTutorial/01/
Best
Feng Pan
On Fri, Mar 24, 2017 at 2:44 PM, Chitrak Gupta <chgupta.mix.wvu.edu> wrote:
> Hi Amber users,
>
> I am simulating a lipid-peptide system. To keep my peptide from interacting
> with lipids in the periodic image, I want to apply a restraint on the
> distance between a protein atom and a lipid atom. From what I understand,
> the only way to apply such restraint is to use "NMR restraints".
>
> Is there a way to apply the restraint only on the z-projection of the
> distance? In principle, I am not concerned with the actual distance between
> lipid and peptide, as long as the z-projection of the distance is below a
> certain upper-bound.
>
>
> Thanks in advance,
> Chitrak.
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--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Fri Mar 24 2017 - 12:30:03 PDT
