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Desmond 3.4.0.2 source code released

已有 3457 次阅读 2013-4-10 02:29 |个人分类:科研笔记|系统分类:科研笔记| code, Source, Desmond, VIPARR4

This new version finally update VIPARR tool from 3.x into 4.x which can handle NBFIX terms in CHARMM 36 protein FF and latest CHARMM 36 LIPIDS FF parameter sets.

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                           Desmond Source Release
                              Desmond 3.4.0.2
                               April 1, 2013

                            D. E. Shaw Research

Desmond
=======

Changes to support compilation on more Linux distributions.

3.4.0.1
=======

This section summarizes the significant changes made in Desmond since the
Desmond 3.0 release.

Features
--------

Configuration error reporting has been improved.  In particular, a key history
is internally maintained so that, when there is a complaint about a missing or
invalid parameter, the user gets a much better idea about where that parameter
is located.  Configuration files for 3.4 are backward compatible.

Desmond now uses the new Random123 random number generator.  One benefit of
this is that random operations across particles return the same results,
independent of the number of processes running.  For example, Desmond now gets
nearly identical results (up to arithmetic error) when running randomized
integrators (Langevin, Brownie) on different numbers of processors.

Desmond is now using the MSYS library for all reading of structure files.  As
a result, a new boot.type optional (for backwards compatibility) flag has been
added to allow (experimental) booting of Maestro files in Desmond through
MSYS.  Currently supported types are 'DMS' and 'MAE' (yes, in theory, you
don't need mae2dms -- in theory).  Developer infrastructure is in place to
support any other type that MSYS can import (i.e., should be fairly easy to
support anything that MSYS supports).

DMS files are read in a more strongly typed fashion.  It used to be that the
types of columns in the DMS file were not checked to see if they matched the
type required by Desmond.  It would do the right thing in some mismatch cases
and the wrong thing in others.  As a result, some DMS files that were produced
by SQLITE3 hacks will likely cause problems.

Some new functions have been added to enhanced_sampling (see guide).  A
long-standing bug in which the 'pow' function was not recognized by the parser
has been fixed.  The enhanced_sampling extension now supports 'whim'
descriptors.

A 'Mixed' thermostat has been added to the Multigrator plugin (see guide).  An
'Antithetic' thermostat has been added to the cadre of basic thermostats (see
guide).  Both Multigrator and Polarization can make use of it.

The extended energy term records the "heat" changes that result from the
plugins remove_com_motion and randomize_velocities, and thus the conservation
of the total energy will persist in the presence of such plugins.

New Gibbs types have been added which support a three charge (chargeA,
chargeB, chargeC) alchemical system, as in force fields where the formal
charges on all atoms are subject to change, rendering all formal charges
alchemical.  This is still mostly an experimental feature.  Gibbs also had a
new alchemical_pair_softcore_es pipeline to do alchemical pair terms with a
softcore functional form.  See guide.

Gibbs nonbonded terms have the option of having their nonbonded correction
corrected to account for the variable presence of ligand terms in FEP binding
calculations (see guide).

To support a certain replica-exchange/FEP workflow, an optional 'deltaE'
parameter has been added to remd-graph (see guide).

The trajectory plugin writes out a VIRIALTENSOR into its frames.  The
trajectory extension also provides the special dbl_trajectory plugin which
will output in DBL_WRAPPED_V_2 format.  vrun in ReleaseDbl will read these
frames back in their full precision, while vrun in Release will always read
these back in single precision.  These features exist mostly to support
debugging and Anton/Desmond comparisons.

A new main loop plugin called virial_breakdown has been added to the
additional_output extension.  It reports a breakdown of virial contributions
across force categories.  This is primarily expected to be used as a debugging
tool for Anton developers, though a brief description is in the users’ guide.

Optimizations were made in both GSE and PME pipelines.  The GSE pipelines now
perform much faster than before and have comparable performance to PME with a
high order.  The performance gap between GSE and PME is substantially more
narrow.

Added a force.nonbonded.suppress_exclusions optional flag (default false)
which allows exclusion injection to be avoided as might be needed for certain
debugging operations.  We do not expect its use outside of this context and do
not document it in the guide.

The 'reshake' flag has been enabled for ReleaseDbl (default to true as in
Release).  Although ReleaseDbl does not need it for constraints, enabling it
causes Desmond to be a bit more robust against initial constraint violations
in the structure file, and thus Release and ReleaseDbl give closer numerical
results in these cases.  The performance impact is negligible.

Bugfixes
--------

Reich water constraints test the water terms to make sure they satisfy certain
symmetry assumptions made by the algorithm.

We used to have particle GID's reported when a particle went missing.  We now
report them again.

The LCn virtual sites had a very subtle non-reversibility bug which prevented
systems with these sites from working reversibly in unconstrained NVE
simulations.

The alchemical nonbonded near terms and softcore pair in Gibbs used to
generator a NaN if two noninteracting alchemical particles wound up on top of
each other.

A long-standing bug in the GSE virial bug has been corrected.  This bug
manifested when the grid-size of the FFT was picked too aggressively (triggers
roughly when the grid spacing equals sigma_s or larger).

Checkpointing does in memory buffering which speeds up the save and loads at
the expensive of a bit of RAM at runtime.  For some systems this was a
dramatic speed up of saving and loading.




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