Hi,
The NFE module can do this, I just gave the example in the tutorial
http://ambermd.org/tutorials/advanced/tutorial31/index.html
the customized reaction coordinate is the Z component of distance,
http://ambermd.org/tutorials/advanced/tutorial31/custom_cv/index.html
Basically if you want to define the z-component of COM you need some coding
but should not be very hard, I have the instructions
to modify the codes in the tutorial.
Best
Feng
On Sat, Jan 18, 2020 at 8:15 AM David Case <david.case.rutgers.edu> wrote:
> Is there a built-in way in pmemd to define a progress variable (aka
> reaction coordinate) for umbrella sampling to be the z-component of the
> center-of-mass of some group of atoms?
>
> We have a lipid bilayer with the normal along the z-axis, and would like
> to estimate a PMF for pulling a peptide out of the membrane.
> Suggestions for other/better ways to do this are also welcome.
>
> ....thx...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 19 2020 - 09:00:01 PST
