blade (c49b1)
BLaDE is a Basic Lambda Dynamics Engine for fast alchemical
simulations on GPUs. BLaDE was designed as a standalone MD engine, but has
also been ported for use as a library in CHARMM. BLaDE can also run
standard molecular dynamics simulations, though the CHARMM OpenMM port is
likely faster for such simulations. BLaDE is optimized for system sizes of
a few to 100k atoms; beyond 1M atoms performance is likely to suffer, and
domdec may be a better platform.
* Syntax | Syntax of the blade commands
* Function | What the syntax means
* Limitations | Some warnings...
simulations on GPUs. BLaDE was designed as a standalone MD engine, but has
also been ported for use as a library in CHARMM. BLaDE can also run
standard molecular dynamics simulations, though the CHARMM OpenMM port is
likely faster for such simulations. BLaDE is optimized for system sizes of
a few to 100k atoms; beyond 1M atoms performance is likely to suffer, and
domdec may be a better platform.
* Syntax | Syntax of the blade commands
* Function | What the syntax means
* Limitations | Some warnings...
Top
Syntax of BLaDE commands
BLaDE [ON | OFF | FILE filename]
ENERgy [energy_opts] BLADE [ABIC]
DYNAmics [dynamics_opts] BLADE [blade_cpt_opts] [ABIC]
blade_cpt_opts::= [PRMC [IPRS int] [PREF real] [PRDV real]]
[FINALT real]
Syntax of BLaDE commands
BLaDE [ON | OFF | FILE filename]
ENERgy [energy_opts] BLADE [ABIC]
DYNAmics [dynamics_opts] BLADE [blade_cpt_opts] [ABIC]
blade_cpt_opts::= [PRMC [IPRS int] [PREF real] [PRDV real]]
[FINALT real]
Top
BLaDE requires a GPU to run, and does not use MPI parallelism. To
parallelize the system over multiple GPUs, use a separate OpenMP thread for
each GPU. Note that BLaDE expects the number of OpenMP threads to be equal
to the number of available GPUs. If there are more OpenMP threads than
GPUs, BLaDE will crash.
1) BLADE can be turned on and off with BLADE ON or BLADE OFF. BLADE ON
overrides domdec and openmm for energy and dynamics calculations. BLaDE is
also maintained as a standalone program with its own scripting language. To
read in a blade script to perform additional BLaDE commands after
initializing the system with charmm but before running dynamics, use BLADE
FILE [filename].
2) Add the BLADE keyword to an energy or dynamics calculation to perform
that calculation with BLaDE. BLaDE does not recognize DYNAMICS CPT
keywords. To run a constant pressure simulation, specify the BLaDE option
PRMC (PRessure Monte Carlo). The options for the Monte Carlo barostat are
IPRS, the frequency to attempt volume changes (default 50 steps), PREF, the
reference pressure in atmospheres (default 1), and PRDV, the standard
deviation of the Gaussian distribution from which volume changes are drawn
in Angstroms cubed (default 100 A^3). The temperature of the Langevin
thermostat is set with FINALT. The ABIC option stands for "assume BLaDE is
current", and will prevent the BLaDE system from reinitializing. Only
spatial and alchemical coordinates and velocities will be updated. If
anything else has changed since the last time BLaDE was called, ABIC will
give incorrect results. Not reinitializing BLaDE can result in significant
performance improvements.
BLaDE requires a GPU to run, and does not use MPI parallelism. To
parallelize the system over multiple GPUs, use a separate OpenMP thread for
each GPU. Note that BLaDE expects the number of OpenMP threads to be equal
to the number of available GPUs. If there are more OpenMP threads than
GPUs, BLaDE will crash.
1) BLADE can be turned on and off with BLADE ON or BLADE OFF. BLADE ON
overrides domdec and openmm for energy and dynamics calculations. BLaDE is
also maintained as a standalone program with its own scripting language. To
read in a blade script to perform additional BLaDE commands after
initializing the system with charmm but before running dynamics, use BLADE
FILE [filename].
2) Add the BLADE keyword to an energy or dynamics calculation to perform
that calculation with BLaDE. BLaDE does not recognize DYNAMICS CPT
keywords. To run a constant pressure simulation, specify the BLaDE option
PRMC (PRessure Monte Carlo). The options for the Monte Carlo barostat are
IPRS, the frequency to attempt volume changes (default 50 steps), PREF, the
reference pressure in atmospheres (default 1), and PRDV, the standard
deviation of the Gaussian distribution from which volume changes are drawn
in Angstroms cubed (default 100 A^3). The temperature of the Langevin
thermostat is set with FINALT. The ABIC option stands for "assume BLaDE is
current", and will prevent the BLaDE system from reinitializing. Only
spatial and alchemical coordinates and velocities will be updated. If
anything else has changed since the last time BLaDE was called, ABIC will
give incorrect results. Not reinitializing BLaDE can result in significant
performance improvements.
Top
BLaDE is designed to be simple and fast, so many features are unavailable.
BLaDE requires PME electrostatics and VFSWITCH van der Waals interactions.
Restraints are not implemented, and the only constraints supported are
hydrogen bond length constraints.
Only a Langevin thermostat (or constant energy) and Monte Carlo barostat
(or constant volume) are supported. If other integrators are requested with
dynamics, the specification is silently ignored and dynamics run with a
Langevin thermostat. All spatial degrees of freedom use the same drag
coefficient (set by scalar fbeta), and all alchemical degrees of freedom
use the same drag coefficient (set by BLOCK LDIN). If drag coefficients
differ, the first atom and the last block prevail. To run a constant energy
simulation, set the drag coefficients to 0.
BLaDE was optimized to run MSLD simulations fast, so most MSLD
functionality in BLOCK is supported. BLaDE can also be used to run
standard, non-alchemical simulations, the number of BLOCKs is just set to 1
internally.
BLaDE is designed to be simple and fast, so many features are unavailable.
BLaDE requires PME electrostatics and VFSWITCH van der Waals interactions.
Restraints are not implemented, and the only constraints supported are
hydrogen bond length constraints.
Only a Langevin thermostat (or constant energy) and Monte Carlo barostat
(or constant volume) are supported. If other integrators are requested with
dynamics, the specification is silently ignored and dynamics run with a
Langevin thermostat. All spatial degrees of freedom use the same drag
coefficient (set by scalar fbeta), and all alchemical degrees of freedom
use the same drag coefficient (set by BLOCK LDIN). If drag coefficients
differ, the first atom and the last block prevail. To run a constant energy
simulation, set the drag coefficients to 0.
BLaDE was optimized to run MSLD simulations fast, so most MSLD
functionality in BLOCK is supported. BLaDE can also be used to run
standard, non-alchemical simulations, the number of BLOCKs is just set to 1
internally.