blade (c49b2)
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]
MINImize [minimize_opts] BLADE
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]
MINImize [minimize_opts] BLADE
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, minimization, 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 can also perform
rudimentary minimization with or without shake. Only the minimization
algorithm, the initial step length (STEP), and the number of steps are read
from standard minimization options. Supported algorithms include steepest
descent (SD) and a BLaDE specific steepest descent finite difference
algorithm with annealing (SDFD). The latter algorithm chooses the search
based on steepest descent, but performs a second energy calculation to
determine the position of the minimum along that direction using a finite
difference approximation. The step length is linearly annealed from the
full distance to the minimum at the start of minimization to 0 percent of
the distance to the minimum at the end of the simulation. This damps out
resonant oscillations that prevent steepest descent from removing large
forces on particles.
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, minimization, 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 can also perform
rudimentary minimization with or without shake. Only the minimization
algorithm, the initial step length (STEP), and the number of steps are read
from standard minimization options. Supported algorithms include steepest
descent (SD) and a BLaDE specific steepest descent finite difference
algorithm with annealing (SDFD). The latter algorithm chooses the search
based on steepest descent, but performs a second energy calculation to
determine the position of the minimum along that direction using a finite
difference approximation. The step length is linearly annealed from the
full distance to the minimum at the start of minimization to 0 percent of
the distance to the minimum at the end of the simulation. This damps out
resonant oscillations that prevent steepest descent from removing large
forces on particles.
Top
BLaDE is designed to be simple and fast, so many features are unavailable.
BLaDE requires PME or VSWITCH electrostatics and VFSWITCH or VSHIFT van der
Waals interactions.
A few restraints are implemented, including absolute position restraints,
and NOE distance restraints. Only restraints involving a single atom or
pair of atoms are supported. The only constraints supported are hydrogen
bond length constraints.
BLaDE supports arbitrary nonorthogonal boxes as well as some types of
virtual sites or lone pairs.
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 or VSWITCH electrostatics and VFSWITCH or VSHIFT van der
Waals interactions.
A few restraints are implemented, including absolute position restraints,
and NOE distance restraints. Only restraints involving a single atom or
pair of atoms are supported. The only constraints supported are hydrogen
bond length constraints.
BLaDE supports arbitrary nonorthogonal boxes as well as some types of
virtual sites or lone pairs.
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.