CPPTRAJ:
-‘replicatecell’: Replicate unit cell in any or all directions.
-‘energy’: Simple energy calculation (faster than imin=5, no PME);
calculate only terms you want.
-‘areapermol’: Simple area per molecule calculation (codifies what is
done in lipid tutorial A16).
-‘checkchirality’: Action for checking amino acid chirality.
-‘volume’: Action for calculating unit cell volume.
-‘multivector’: Action for calculating multiple vectors (e.g. all N-H vectors).
-Reference structures can be manipulated (like COORDS set).
-Some math operations can be performed on/between data sets (e.g. D0 =
D1 + 2.3 etc).
-Non-linear curve fitting
-‘minimage’: distance to next closest unit cell (atoms or center of
mass), along with atom IDs.
-‘vector minimage’: shortest vector between two points (like ‘distance’).
-Imaging in 'hbond' command (distances and angles).
-Non-orthogonal grids, normalize grids by density.
-Vast improvements to 'nativecontacts' command, including time series
generation.
-Combine coordinates (essentially reverse of strip)
-Clustering: K-means, symmetric RMSD metric, pseudo-F and silhouette
clustering metrics
-Improvements to 'atommap' and 'symmrmsd' commands.
On Mon, Apr 13, 2015 at 11:44 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Scalable multigrid algorithm in periodic linear PB calculations for
> implicit membrane systems
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Mon, Apr 13, 2015 at 10:24 AM, Jason Swails <jason.swails.gmail.com> wrote:
>> Not all contributions are mine (although if I've forgotten any, it's likely
>> because they weren't :)
>>
>> - sander API
>> - numerous ParmEd enhancements and significant parsing speed-ups
>> - chamber -> ParmEd, better support for CHARMM force field (particularly
>> NBFIX)
>> - pdb4amber improvements (e.g., can now use reduce, auto tautomer ID)
>> - major improvements to cpptraj (Dan can summarize any major bullet points)
>> - pytraj -- Python bindings to cpptraj
>> - pymsmt -- MCPB.py for modeling metal complexes
>> - Optimized nucleic acid GBneck2 parameters
>> - trivalent and tetravalent metal ion parameters and 12-6-4 monovalent ion
>> parameters
>> - Major sander cleanup
>> - gbnsr6 program for improved GB model in single-point calculations
>> - OPC water model
>> - Support for clang compiler and dragonegg GCC plugin
>> - Implicit membrane support in FEW and PBSA (although I think it's only
>> *new* in FEW)
>>
>> Can't think of any more at the moment.
>>
>>
>> On Mon, Apr 13, 2015 at 1:02 PM, David A Case <case.biomaps.rutgers.edu>
>> wrote:
>>
>>> Please send me short bullet points outlining significant changes in
>>> AmberTools
>>> 15 (vs AmberTools14). I will collect these into info for the web site and
>>> for
>>> the release announcement.
>>>
>>> ....thx...dave
>>>
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Apr 14 2015 - 09:00:07 PDT
