Hello Amber Devs
Here I just have finished some new updates for the NFE modules in both
SANDER and PMEMD.
The main update is that I add the contribution of potential energies from
restraints in NFE modules (could from several different methods).
Right now these energies will be written out to the mdout files in the
frequency decided by ntpr. The contributions from different methods
are classified. You can check the format in the new updated test files
test/nfe or test/nfe/cuda.
Also since these energies are included, REMD methods which relates with
potential energy (like T-REMD or H-REMD) are now compatible
with the NFE module. Based on this update, one important function could be
the users can run Umbrella Sampling with H-REMD using a
variety choice of reaction coordinates like Center of Mass dihedral, Radius
of Gyration, RMSD, etc. And also these can all run with GPUs.
I got several emails from users during this year who has similar requests
and that's my motive to finished those updates.
Besides, I fixed several bugs in the NFE module, as reported by users. And
a bug in H-REMD in pmemd, which may lead to wrong velocities
and forces because of new atom redistribution.
The updates have been merged to the master branch, and should soon be
applied to Amber18 and AmberTools18 by the patches.
Best regards
Feng
--
Feng Pan
Post Doc
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Sat Sep 29 2018 - 21:00:03 PDT
