mirror of
https://git.FreeBSD.org/ports.git
synced 2024-11-28 01:06:17 +00:00
fb16dfecae
Commit b7f05445c0 has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner)
14 lines
987 B
Plaintext
14 lines
987 B
Plaintext
ProtoMol is an object-oriented, component based, framework for molecular
|
|
dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force
|
|
fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is
|
|
designed for high flexibility, easy extendibility and maintenance, and high
|
|
performance demands, including parallelization. The technique of multiple
|
|
time-stepping is used to improve long-term efficiency. The use of fast
|
|
electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME),
|
|
and Multigrid (MG) summation further enhances performance. Longer time steps
|
|
are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover,
|
|
and Langevin integrators. In addition, ProtoMol has been designed to interact
|
|
with VMD, a visualization engine developed by the University of Illinois that is
|
|
used for displaying large biomolecular systems in three dimensions. ProtoMol is
|
|
freely distributed software, and the source code is available.
|