rush (c49b1)
RUSH: A simple implicit-solvent force-field for protein simulation
Olgun Guvench (oguvench@post.harvard.edu)
Charles L. Brooks III (brookscl@umich.edu)
RUSH is a simple implicit-solvent force-field that adds terms
to the bonded portion (bond + angle + dihe + impr + urey) of the
all-atom CHARMM22 force field to account for volume-exclusion (_R_epulsion),
the hydrophobic effect (_U_nburied _S_urface), and intra-molecular
and protein-solvent hydrogen-bonding (_H_ydrogen-bonding) (hence
_R_ _U_ _S_ _H_).
See:
Guvench and Brooks. "Folding the Trp-cage mini-protein to atomic
resolution: Searching parameter space for a free-energy minimum".
J. Chem. Phys. ??? (2006)
* Overview | Overview of the steps involved in applying the force field
* Syntax | Syntax of the RUSH command
* Description | Description of the RUSH command
* Restrictions | Restrictions on usage
* Notes | Implementation and usage notes
* Examples | Usage examples
Olgun Guvench (oguvench@post.harvard.edu)
Charles L. Brooks III (brookscl@umich.edu)
RUSH is a simple implicit-solvent force-field that adds terms
to the bonded portion (bond + angle + dihe + impr + urey) of the
all-atom CHARMM22 force field to account for volume-exclusion (_R_epulsion),
the hydrophobic effect (_U_nburied _S_urface), and intra-molecular
and protein-solvent hydrogen-bonding (_H_ydrogen-bonding) (hence
_R_ _U_ _S_ _H_).
See:
Guvench and Brooks. "Folding the Trp-cage mini-protein to atomic
resolution: Searching parameter space for a free-energy minimum".
J. Chem. Phys. ??? (2006)
* Overview | Overview of the steps involved in applying the force field
* Syntax | Syntax of the RUSH command
* Description | Description of the RUSH command
* Restrictions | Restrictions on usage
* Notes | Implementation and usage notes
* Examples | Usage examples
Top
Usage overview: The steps involved in using the RUSH force field
The basic steps to use the RUSH force field are:
1) read in RUSH-modified versions of the CHARMM22 protein topology and
parameter files and the RUSH cmap parameter file (the appropriate
non-bond list values are set in the parameter file)
2) build the appropriate PSF and read in / build the coordinates
3) use the RUSH keyword to initialize the subroutines and specify
parameters other than the defaults
4) use "skipe all excl bond angl urey dihe impr rrep rpho rhbn rbdo rbac
raro cmap" to turn on the proper combination of energy terms
5) do energy, minimization (first derivative methods _only_), and
dynamics calculations
To turn off RUSH and use the CHARMM22 force field:
1) use "RUSH off" to reset the subroutines and release any memory
used by RUSH
2) use "SKIPE none" to reactivate Lennard-Jones, electrostatic, etc
energy terms
3) delete all atoms
4) read in the original CHARMM22 force field topology and parameter
files to replace the RUSH topologies and parameters and non-bond
parameters
5) proceed as usual
Usage overview: The steps involved in using the RUSH force field
The basic steps to use the RUSH force field are:
1) read in RUSH-modified versions of the CHARMM22 protein topology and
parameter files and the RUSH cmap parameter file (the appropriate
non-bond list values are set in the parameter file)
2) build the appropriate PSF and read in / build the coordinates
3) use the RUSH keyword to initialize the subroutines and specify
parameters other than the defaults
4) use "skipe all excl bond angl urey dihe impr rrep rpho rhbn rbdo rbac
raro cmap" to turn on the proper combination of energy terms
5) do energy, minimization (first derivative methods _only_), and
dynamics calculations
To turn off RUSH and use the CHARMM22 force field:
1) use "RUSH off" to reset the subroutines and release any memory
used by RUSH
2) use "SKIPE none" to reactivate Lennard-Jones, electrostatic, etc
energy terms
3) delete all atoms
4) read in the original CHARMM22 force field topology and parameter
files to replace the RUSH topologies and parameters and non-bond
parameters
5) proceed as usual
Top
Syntax of the RUSH command
Initialization:
RUSH [PHOB <real>] [HBND <real>] [BDON <real>] [BACC <real>] -
[KARO <real>] [CARO <real>] [DRMX <real>]
Clean-up:
RUSH OFF
Syntax of the RUSH command
Initialization:
RUSH [PHOB <real>] [HBND <real>] [BDON <real>] [BACC <real>] -
[KARO <real>] [CARO <real>] [DRMX <real>]
Clean-up:
RUSH OFF
Top
Keyword Default Purpose
PHOB 0.00072 multiplier for the hydrophobic surface-area term
(kcal/(mol*angstrom**7/2)
HBND -5.1 intra-molecular hydrogen bond strength (kcal/mol)
BDON 0.04 burial penalty for hydrogen-bond donors (kcal/mol)
BACC 0.04 burial penalty for hydrogen-bond acceptors (kcal/mol)
KARO 0.00 multiplier for force-shifted Coulomb attraction between
aromatic moieties (unitless)
CARO 0.00 cutoff for force-shifted Coulomb attraction between
aromatic moieties (angstrom)
DRMX 0.50 minimum atomic motion for update of RUSH-associated
neighbor-lists (angstrom)
OFF n/a release heap used by RUSH, reset the RUSH-associated
global variables (including energies), and skip RUSH
energy terms during subsequent energy/derivative
calculations
Keyword Default Purpose
PHOB 0.00072 multiplier for the hydrophobic surface-area term
(kcal/(mol*angstrom**7/2)
HBND -5.1 intra-molecular hydrogen bond strength (kcal/mol)
BDON 0.04 burial penalty for hydrogen-bond donors (kcal/mol)
BACC 0.04 burial penalty for hydrogen-bond acceptors (kcal/mol)
KARO 0.00 multiplier for force-shifted Coulomb attraction between
aromatic moieties (unitless)
CARO 0.00 cutoff for force-shifted Coulomb attraction between
aromatic moieties (angstrom)
DRMX 0.50 minimum atomic motion for update of RUSH-associated
neighbor-lists (angstrom)
OFF n/a release heap used by RUSH, reset the RUSH-associated
global variables (including energies), and skip RUSH
energy terms during subsequent energy/derivative
calculations
Top
The following will not work or give incorrect results:
- anything that requires 2nd derivatives
- periodic boundary conditions, images, etc.
- the free energy modules (pert, tsm, block)
- parallel CHARMM
The following will not work or give incorrect results:
- anything that requires 2nd derivatives
- periodic boundary conditions, images, etc.
- the free energy modules (pert, tsm, block)
- parallel CHARMM
Top
The hydrogen masses are set to 12.01 amu, a holdover from
early in the development of the force field when a single-sided
harmonic potential was used to model volume exclusion ( as opposed
to the current implementation, which employs the repulsive part
of the Weeks-Chandler-Andersen decomposition of the CHARMM22
Lennard-Jones term) and required the increased hydrogen mass to
allow for energy conservation with a 2-fs timestep. This does not
affect the thermodynamic properties of the system owing to the lack
of atomic mass in the configurational part of the partition function.
The dynamic properties are affected, but this is a moot point since
the solvent is modeled implicitly. From a practical perspective, using
SHAKE is optional: a 2-fs timestep will achieve energy conservation
with or without SHAKE owing to the heavy hydrogens. From a philosophical
perspective, some may choose to use SHAKE since hydrogen has significant
quantum-mechanical character at room temperature. All development and
testing was done without SHAKE.
The surface-area based hydrophobic term is discontinuous in the first
derivatives. This occassionally causes problems with conjugate gradient
minimization; stick to steepest-descent. Energy conservation during
MD is not a problem despite the discontinuity. Using a 2-fs timestep,
the average total energy for a constant energy simulation of the trpzip2
designed beta hairpin after equilibration to 298 K is 631.7 kcal/mol
for the first 20-ps interval and 632.5 kcal/mol for the last 20-ps
interval of a 100-ps simulation.
PSF files from the standard CHARMM22 all-atom force field are NOT
compatible with RUSH. Use the rush topology file to build the PSF.
The aromatic energy term RARO was added subsequent to the publication of
the original model. Its purpose is to maintain the proper geometry of
interacting aromatic residues (Guvench and Brooks. "Tryptophan side chain
electrostatic interactions determine edge-to-face vs parallel-displaced
tryptophan side chain geometries in the designed beta-hairpin tripzip2".
J. Am. Chem. Soc. 127:4668-4674 (2005)) It is simply a force-switched
electrostatic term (Steinback and Brooks. "New spherical-cutoff methods
for long-range forces in macromolecular simulation". J. Comput. Chem. 15:
667-683 (1994)) that is applied to all atoms in the topology file with
non-zero charge, which currently comprise only the atoms of the
aromatic moieties of the Phe, Trp, and Tyr sidechains and the Tyr -OH
group. The default for KARO is 0.0, so that this term is not included
in the calculation.
The hydrogen masses are set to 12.01 amu, a holdover from
early in the development of the force field when a single-sided
harmonic potential was used to model volume exclusion ( as opposed
to the current implementation, which employs the repulsive part
of the Weeks-Chandler-Andersen decomposition of the CHARMM22
Lennard-Jones term) and required the increased hydrogen mass to
allow for energy conservation with a 2-fs timestep. This does not
affect the thermodynamic properties of the system owing to the lack
of atomic mass in the configurational part of the partition function.
The dynamic properties are affected, but this is a moot point since
the solvent is modeled implicitly. From a practical perspective, using
SHAKE is optional: a 2-fs timestep will achieve energy conservation
with or without SHAKE owing to the heavy hydrogens. From a philosophical
perspective, some may choose to use SHAKE since hydrogen has significant
quantum-mechanical character at room temperature. All development and
testing was done without SHAKE.
The surface-area based hydrophobic term is discontinuous in the first
derivatives. This occassionally causes problems with conjugate gradient
minimization; stick to steepest-descent. Energy conservation during
MD is not a problem despite the discontinuity. Using a 2-fs timestep,
the average total energy for a constant energy simulation of the trpzip2
designed beta hairpin after equilibration to 298 K is 631.7 kcal/mol
for the first 20-ps interval and 632.5 kcal/mol for the last 20-ps
interval of a 100-ps simulation.
PSF files from the standard CHARMM22 all-atom force field are NOT
compatible with RUSH. Use the rush topology file to build the PSF.
The aromatic energy term RARO was added subsequent to the publication of
the original model. Its purpose is to maintain the proper geometry of
interacting aromatic residues (Guvench and Brooks. "Tryptophan side chain
electrostatic interactions determine edge-to-face vs parallel-displaced
tryptophan side chain geometries in the designed beta-hairpin tripzip2".
J. Am. Chem. Soc. 127:4668-4674 (2005)) It is simply a force-switched
electrostatic term (Steinback and Brooks. "New spherical-cutoff methods
for long-range forces in macromolecular simulation". J. Comput. Chem. 15:
667-683 (1994)) that is applied to all atoms in the topology file with
non-zero charge, which currently comprise only the atoms of the
aromatic moieties of the Phe, Trp, and Tyr sidechains and the Tyr -OH
group. The default for KARO is 0.0, so that this term is not included
in the calculation.
Top
* 1) read in the RUSH topology, parameter, and cmap files
* 2) read in the protein psf and coordinates
* 3) turn on RUSH
* 4) do a minimization and energy calculation
* 5) turn off RUSH and exit
open unit 1 read form name @TOPPAR/rush/top_rush_058.inp
read rtf card unit 1
close unit 1
open unit 1 read form name @TOPPAR/rush/par_rush_058.inp
read param card unit 1
close unit 1
open unit 1 read form name @TOPPAR/rush/par_rush_058_a.cmap
read param append card unit 1
close unit 1
open unit 1 read form name ./@PDB.psf
read psf card unit 1
close unit 1
open unit 1 read form name ./@PDB.pdb
read coor pdb unit 1
close unit 1
rush
skipe all excl -
bond angl urey dihe impr rrep rpho rhbn rbdo rbac raro cmap
minimize sd nstep 1000 tolgrd 0.1
energy
rush off
stop
* 1) read in the RUSH topology, parameter, and cmap files
* 2) read in the protein psf and coordinates
* 3) turn on RUSH
* 4) do a minimization and energy calculation
* 5) turn off RUSH and exit
open unit 1 read form name @TOPPAR/rush/top_rush_058.inp
read rtf card unit 1
close unit 1
open unit 1 read form name @TOPPAR/rush/par_rush_058.inp
read param card unit 1
close unit 1
open unit 1 read form name @TOPPAR/rush/par_rush_058_a.cmap
read param append card unit 1
close unit 1
open unit 1 read form name ./@PDB.psf
read psf card unit 1
close unit 1
open unit 1 read form name ./@PDB.pdb
read coor pdb unit 1
close unit 1
rush
skipe all excl -
bond angl urey dihe impr rrep rpho rhbn rbdo rbac raro cmap
minimize sd nstep 1000 tolgrd 0.1
energy
rush off
stop