Amber16及AmberTools16发布

sobereva

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)
• Gaussian Accelerated Molecular Dynamics (CPU, GPU)
• Support for external electric fields (CPU)
• Expanded umbrella sampling support (GPU)
• Constant pH supported with replica exchange along pH coordinate (GPU)
• Support for gas phase MD (igb=6) (CPU, GPU)
• Support and significant performance improvements for the latest Kepler, Maxwell and Pascal GPUs from NVIDIA.
  

laoman

五一劳动节就更新了~~

我本是个娃娃

老师，相较于GMX，Amber的优缺点有哪些，两者的不同又是什么？
另，动力学班的相关事宜都敲定了吗？

sobereva

我本是个娃娃 发表于 2016-5-1 10:52
老师，相较于GMX，Amber的优缺点有哪些，两者的不同又是什么？
另，动力学班的相关事宜都敲定了吗？

没敲定。

Amber速度和灵活性比gromacs差，而且PMEMD模块收费，优点是高级功能更多，比如能做Constant PH、直接支持半经验级别的QM/MM、有antechamber生成小分子拓扑文件等。