ms-evb (c44b1)
Multi-State Empirical Valence Bond
David Glowacki, Robert Arbon
The multi-state empirical valence bond (MS-EVB) module of CHARMM
offers an efficient method for representing reactive potential energy
surfaces, e.g., such as those which occur in enzymes, where a system
moves from a reactant topology to a product topology. For a given set
of Cartesian coordinates at a particular timestep, the CHARMM EVB
implementation works by evaluating potential energies and forces in
parallel for multiple topological replicas of the same set of atomic
Cartesian coordinates. The potential energy corresponding to each
topology is used to populate the diagonal elements of a matrix H. The
off-diagonal coupling elements of H are calculated as functions which
depend on a user-specified set of collective variables which undergo
significant change as the system switches between topologies (usually
bond distances). Having constructed H, the system potential energy,
taken to be some linear combination of the potential energies of each
topological replica, is calculated as the lowest eigenvalue of this
matrix.
This CHARMM EVB implementation allows one to construct a potential
energy surface which smoothly connects different topologies - e.g.,
from a reactant to a product and vice-versa. Forces on this potential
energy surface are obtained using the Hellmann-Feynman relationship,
giving continuous gradients, and good energy conservation. The CHARMM
EVB implementation utilises MPI to parallelize the energy and force
calculations of each topological replica at any given timestep,
achieving near-linear scaling in the number of topological replicas.
It allows for an arbitrary number of topological replicas limited only
by the number of MPI threads allowed by the system architecture. It
allows the user to select from a range of functional forms in the
coupling elements, including constants, 1D and 2D Gaussian
functions. Coupling elements of this form can be used to construct
reactive potential energy surfaces, solute spectra, and vibrational
frequencies comparable in quality to high-level electronic structure
theory or QM/MM approaches.
References:
1) Glowacki DR, Orr-Ewing AJ and Harvey, JN, J Chem Phys, 143, 044120 (2015), DOI:10.1063/1.4926996
2) Glowacki DR, Orr-Ewing AJ and Harvey, JN, J Chem Phys, 134, 214508 (2011), DOI:10.1063/1.3595259
------------------------------------------------------------------
NOTES ON BUILDING THE ENSEMBLE CODE:
For gnu compilers using the new CMake build system:
$> ./configure -a ENSEMBLE
$> make -C build/cmake install
------------------------------------------------------------------
* Syntax | Syntax of the ENSEMBLE EVB command
* General Description | General info on I/O and other practical matters
* Test Cases | Description of c41 tests
David Glowacki, Robert Arbon
The multi-state empirical valence bond (MS-EVB) module of CHARMM
offers an efficient method for representing reactive potential energy
surfaces, e.g., such as those which occur in enzymes, where a system
moves from a reactant topology to a product topology. For a given set
of Cartesian coordinates at a particular timestep, the CHARMM EVB
implementation works by evaluating potential energies and forces in
parallel for multiple topological replicas of the same set of atomic
Cartesian coordinates. The potential energy corresponding to each
topology is used to populate the diagonal elements of a matrix H. The
off-diagonal coupling elements of H are calculated as functions which
depend on a user-specified set of collective variables which undergo
significant change as the system switches between topologies (usually
bond distances). Having constructed H, the system potential energy,
taken to be some linear combination of the potential energies of each
topological replica, is calculated as the lowest eigenvalue of this
matrix.
This CHARMM EVB implementation allows one to construct a potential
energy surface which smoothly connects different topologies - e.g.,
from a reactant to a product and vice-versa. Forces on this potential
energy surface are obtained using the Hellmann-Feynman relationship,
giving continuous gradients, and good energy conservation. The CHARMM
EVB implementation utilises MPI to parallelize the energy and force
calculations of each topological replica at any given timestep,
achieving near-linear scaling in the number of topological replicas.
It allows for an arbitrary number of topological replicas limited only
by the number of MPI threads allowed by the system architecture. It
allows the user to select from a range of functional forms in the
coupling elements, including constants, 1D and 2D Gaussian
functions. Coupling elements of this form can be used to construct
reactive potential energy surfaces, solute spectra, and vibrational
frequencies comparable in quality to high-level electronic structure
theory or QM/MM approaches.
References:
1) Glowacki DR, Orr-Ewing AJ and Harvey, JN, J Chem Phys, 143, 044120 (2015), DOI:10.1063/1.4926996
2) Glowacki DR, Orr-Ewing AJ and Harvey, JN, J Chem Phys, 134, 214508 (2011), DOI:10.1063/1.3595259
------------------------------------------------------------------
NOTES ON BUILDING THE ENSEMBLE CODE:
For gnu compilers using the new CMake build system:
$> ./configure -a ENSEMBLE
$> make -C build/cmake install
------------------------------------------------------------------
* Syntax | Syntax of the ENSEMBLE EVB command
* General Description | General info on I/O and other practical matters
* Test Cases | Description of c41 tests
Top
Initialize ENSEMBLE:
--------------------
ENSEMBLE NENSEM integer
General commands:
-----------------
ENSEMBLE SYNC
ENSEMBLE SEED [ROOT integer]
Force-field averaging (used for "multi-Go", for example)
--------------------------------------------------------
ENSEMBLE EXPAvg BETA real [ UNIT real ] -
OFFSet real_1 real_2 ... real_nensem
Initialize ENSEMBLE:
--------------------
ENSEMBLE NENSEM integer
General commands:
-----------------
ENSEMBLE SYNC
ENSEMBLE SEED [ROOT integer]
Force-field averaging (used for "multi-Go", for example)
--------------------------------------------------------
ENSEMBLE EXPAvg BETA real [ UNIT real ] -
OFFSet real_1 real_2 ... real_nensem
Top
The following section describes the keywords of the ENSEMBLE command.
General Description
===================
Ensemble enabled executables run exactly the same as normal parallel
command is. A charmm script will be processed in the normal parallel
way until the ensemble initializing command is given. Once ensemble is
initialized for N replicas, there are N replicas of charmm running
where the total processors are split evenly among the replicas. (***
The total number of processors must be evenly divisable by the number
of replicas. ***)
Once running in ensemble mode, each replica runs independently at
first, each reading the default input stream. Each replica produces
its default output to an output file charmm.out.xxx, where xxx is the
replica number (excepting the 0th replica which still goes to stdout)
from 1 to N-1.
Each replica can open and close files independently. Take care to not
open the same file for writing (such as dcd or restart files) on
different replicas, see example below.
Each replica can stream a new input file, allowing independent
simulations to run out of the a large number of processors in the same
batch run.
Initializing ENSEMBLE
-----------------------
The command
ensemble nensem 2
will break the processors into 2 replicas of the current state of the
charmm run, giving 1/2 of the processors to each replica. The replicas
are numbered 0,1. The output for rep 0 still goes to stdout, while
the other go to charmm.out.001. The
replicas keep reading the input file (though independently) unless
directed to stream another input file. The identity of the replica can
be determined from ?whoiam and the total number of replicas can be
determined from ?nensem.
set numrep ?nensem
set myrep ?whoiam
Each node reads the input file itself and each node maintains a
completely independent copy of all data. This allows dynamics to be
run much as usual, with all nodes happily unaware of the others, apart
from the communication entailed in replica-exchange or force-field
averaging. A few points about I/O.
------------------------------------------------------------------
trajectories (coord/velocities/..)
restart files
energy files from dynamics runs
any other dynamics output which will differ between replicas
coordinate writing
experimental data files for HQBM
Files opened for reading by all reps will be opened by each rep in
read-only mode, each rep opening the file and reading it
independently. This may cause io delays for huge numbers of reps.
Some Initialization notes
-------------------------
For most ensemble averaged restraints, starting all replicas with the same
coordinates and velocities this is a waste of time (and is one pathological
case where an N-replica simulation will behave exactly like a single replica).
Thusly, one should assign either or both different random seeds (see below) and
different starting coordinates to different replicas. Bear in mind that not all
integration schemes in CHARMM actually use a random seed from the dyna command
(e.g. NOSE does not, but LEAP VERLET does).
e.g. for assigning different seeds
if ?whoiam .eq. 0 set seed 23832
if ?whoiam .eq. 1 set seed 9375283
etc...
Then use "dyna start ... iseed @seed ..."
Syntax
------
ensemble evb
SHFT 0 @E1
SHFT 1 @E2
COUP 0 1 CONS @CONS
COUP 0 1 GAUS TWOD @A @R01 @C1 SELE R1 END @THETA @R02 @C2 SELE R2 END
envbi
The following section describes the keywords of the ENSEMBLE command.
General Description
===================
Ensemble enabled executables run exactly the same as normal parallel
command is. A charmm script will be processed in the normal parallel
way until the ensemble initializing command is given. Once ensemble is
initialized for N replicas, there are N replicas of charmm running
where the total processors are split evenly among the replicas. (***
The total number of processors must be evenly divisable by the number
of replicas. ***)
Once running in ensemble mode, each replica runs independently at
first, each reading the default input stream. Each replica produces
its default output to an output file charmm.out.xxx, where xxx is the
replica number (excepting the 0th replica which still goes to stdout)
from 1 to N-1.
Each replica can open and close files independently. Take care to not
open the same file for writing (such as dcd or restart files) on
different replicas, see example below.
Each replica can stream a new input file, allowing independent
simulations to run out of the a large number of processors in the same
batch run.
Initializing ENSEMBLE
-----------------------
The command
ensemble nensem 2
will break the processors into 2 replicas of the current state of the
charmm run, giving 1/2 of the processors to each replica. The replicas
are numbered 0,1. The output for rep 0 still goes to stdout, while
the other go to charmm.out.001. The
replicas keep reading the input file (though independently) unless
directed to stream another input file. The identity of the replica can
be determined from ?whoiam and the total number of replicas can be
determined from ?nensem.
set numrep ?nensem
set myrep ?whoiam
Each node reads the input file itself and each node maintains a
completely independent copy of all data. This allows dynamics to be
run much as usual, with all nodes happily unaware of the others, apart
from the communication entailed in replica-exchange or force-field
averaging. A few points about I/O.
------------------------------------------------------------------
trajectories (coord/velocities/..)
restart files
energy files from dynamics runs
any other dynamics output which will differ between replicas
coordinate writing
experimental data files for HQBM
Files opened for reading by all reps will be opened by each rep in
read-only mode, each rep opening the file and reading it
independently. This may cause io delays for huge numbers of reps.
Some Initialization notes
-------------------------
For most ensemble averaged restraints, starting all replicas with the same
coordinates and velocities this is a waste of time (and is one pathological
case where an N-replica simulation will behave exactly like a single replica).
Thusly, one should assign either or both different random seeds (see below) and
different starting coordinates to different replicas. Bear in mind that not all
integration schemes in CHARMM actually use a random seed from the dyna command
(e.g. NOSE does not, but LEAP VERLET does).
e.g. for assigning different seeds
if ?whoiam .eq. 0 set seed 23832
if ?whoiam .eq. 1 set seed 9375283
etc...
Then use "dyna start ... iseed @seed ..."
Syntax
------
ensemble evb
SHFT 0 @E1
SHFT 1 @E2
COUP 0 1 CONS @CONS
COUP 0 1 GAUS TWOD @A @R01 @C1 SELE R1 END @THETA @R02 @C2 SELE R2 END
envbi
Top
TESTCASES:
=============================================
c41test:
--------
evb_dynamics.inp
evb_scan.inp
TESTCASES:
=============================================
c41test:
--------
evb_dynamics.inp
evb_scan.inp