标题: Amber16及AmberTools16发布 [打印本页] 作者Author: sobereva 时间: 2016-5-1 10:02 标题: Amber16及AmberTools16发布 The Amber development team is pleased to announce the release of Amber16
and AmberTools16. These are significant updates from the the previous
releases; an overview of what is changed is available at: http://ambermd.org
Briefly, there are new force fields, improved workflows for system preparation
and analyis, and major updates to the sampling and free energy capabilities of
the pmemd program.
The Amber 2016 Reference Manual is avialable online, both for reference, and
if you want to see if Amber might fit your needs: http://ambermd.org/doc12/Amber16.pdf
As in earlier releases, AmberTools16 is distributed under an open source
license, whereas Amber16 requires users to obtain a license from UCSF.
To get AmberTools16, go to http://ambermd.org/#AmberTools, and click on
"Download AmberTools16".
To license Amber16, please visit http://ambermd.org/#obtain, and follow the
instructions there.
Thanks to everyone on the Amber team who worked really hard to get this
done. Special shout-out to Jason Swails, Hai Nguyen and Scott Brozell for
help in preparing the release. See http://ambermd.org/contributors.html
for a fuller list of who has contributed.
....dave case
for the Amber development team
AmberTools16新特征
Major update to the general Amber force field (GAFF2)
ff15ipq protein force field added
Improved support for the "12-6-4" potential model for monatomic ions.
Improved leaprc files for specifying which force fields to use.
Generation of an API for sander and cpptraj, allowing their functionality to be accessed by third-party programs. Examples include the PHENIX suite of crystallographic refinement programs, and our own new pytraj program, which supports novel ways to do trajectory analysis.
Significant improvments and "real-life" examples for the Low-Mode (LMOD) conformational search routines.
Improved workflow for system preparation and validation.
Periodic version of the 3D-RISM integral equation codes.
Codes to compute SAXS and WAXS data from MD or 3D-RISM calculations.
Support for the new NMR Exchange Format (NEF) formats for NMR restraints.
Continued updates and extensions to the cpptraj program for trajectory analysis:
Improved parallelization: Introduction of cross-trajectory parallelizaion and hybid MPI/Openmp
esander action: links to the sander API to extract energies for analysis
Updated nastruct and diffusion actions
Amber16提供的PMEMD的新特征
Semi-Isotropic Pressure Scaling (GPU)
Charmm VDW Force Switch (CPU, GPU)
Enhanced NMR Restraint support + R^6 averaging support (GPU)
