consph (c48b1)
Monte-carlo method for constant pH simulations
Tim Miller, Ana Damjanovic, Satoru Itoh, and Bernard R. Brooks
If you use this code, please cite:
Itoh SG, Damjanovic A, Brooks BR. Proteins. 79, 3420-3436 (2011).
* Introduction | Overview of the constant pH Monte Carlo method
* Syntax | Syntax of the Constant pH code
* Notes | Usage notes
Tim Miller, Ana Damjanovic, Satoru Itoh, and Bernard R. Brooks
If you use this code, please cite:
Itoh SG, Damjanovic A, Brooks BR. Proteins. 79, 3420-3436 (2011).
* Introduction | Overview of the constant pH Monte Carlo method
* Syntax | Syntax of the Constant pH code
* Notes | Usage notes
Top
The constant pH code is designed to allow the running of a molecular
dynamics simulation with a fixed pH. What this means is that titratable
groups can protonate and deprotonate over the course of the simulation in
a manner dictated by the specified pH value. In order to accomplish this, the
dynamics simulation is periodically interrupted (the frequency can be
determined by the user), and at least one Monte Carlo trial is run that
attempts to change the protonation state of one of the titratable
residues. In this implementation, the user must indicate to CHARMM which
residues may have their protonation state change, which allows for
completely flexibility (e.g. if it is known that a particular residue
never changes its protonation state). This is done via the CNSPh
command (see below).
The code has been tested with standard MD and Langevin dynamics
using the LEAPfrog and VVER integrators. Other integrators have not
been tested, but should work. It is compatible with the existing
CPT code in CHARMM, but image support has not been tested and may
have issues. We have tested with the GBSW and GBMV implicit solvent
methods. The implementation has been parallelized.
The discrete state constant pH is now included by default in
used, then code allowing for replica exchange in pH space will also be
compiled (» repdstr for further details). The constant pH Monte
Carlo procedure will *not* be applied on time steps where a pH replica
exchange occurs.
The constant pH code is designed to allow the running of a molecular
dynamics simulation with a fixed pH. What this means is that titratable
groups can protonate and deprotonate over the course of the simulation in
a manner dictated by the specified pH value. In order to accomplish this, the
dynamics simulation is periodically interrupted (the frequency can be
determined by the user), and at least one Monte Carlo trial is run that
attempts to change the protonation state of one of the titratable
residues. In this implementation, the user must indicate to CHARMM which
residues may have their protonation state change, which allows for
completely flexibility (e.g. if it is known that a particular residue
never changes its protonation state). This is done via the CNSPh
command (see below).
The code has been tested with standard MD and Langevin dynamics
using the LEAPfrog and VVER integrators. Other integrators have not
been tested, but should work. It is compatible with the existing
CPT code in CHARMM, but image support has not been tested and may
have issues. We have tested with the GBSW and GBMV implicit solvent
methods. The implementation has been parallelized.
The discrete state constant pH is now included by default in
used, then code allowing for replica exchange in pH space will also be
compiled (» repdstr for further details). The constant pH Monte
Carlo procedure will *not* be applied on time steps where a pH replica
exchange occurs.
Top
Command syntax:
I/O:
READ CPH CARD UNIT <int> ! Read constant pH parameter file.
Defining titratable groups:
CNSPh {ADD [atom-selection]}
{DEL [atom-selection]}
{CLEAr }
ADD -- Any residue returned by the selection is added to the list
of titratable residues.
DEL -- Any residue returned by the selection is removed from the
list of titratable residues, if present.
CLEAr -- The list of titratable residues is emptied.
Running dynamics with constant pH:
DYNAmics ... PHCONS consph-spec
consph-spec::= PHEXCF <int> PHMCTR <int> [PHUNUM <int>] PHVAL <real>
[ IUNPHR <int> ] [ IUNPHw <int> ] [ PHTEMP <real> ]
[ IPHRSV <int> ]
keyword explanation
------- -----------
PHEXCF Frequency at which to attempt to change the titration state
of the system. Every PHEXCF steps, the dynamics will be
interrupted and the monte carlo procedure run.
PHMCTR The number of Monte Carlo trials to run. As of the current
implementation, the code picks a random residue of those
marked titratable to modify at each step.
PHUNUM The unit to write the current state of the system to at
each step. The syntax of the resulting file is given below.
The default is to not write any file.
PHVAL The pH value at which the simulation is performed.
PHTEMP Temperature to use in the pH exchange equation. If left
unset or if the value given is less than 0, the instantaneous
temperature of the system is used.
IUNPHR Unit to read a restart file from for use with constant pH (NB
the restart file for constant pH is kept separately from the
dynamics restart file).
IUNPHW Unit to write a restart file to for use with constant pH.
IPHRSV Writes a constant pH reservoir file to the specified unit number
for later use with pH reservoir replica exchange (see
repdstr.info for details). An entry will be written every
NSAVC time steps. Note this is only implemented for the
verlet and leapfrog verlet integrators.
Parameter file syntax:
The Constant pH parameter file follows regular CHARMM syntax conventions
(i.e. it must start with a title, and comment lines must begin with an
exclamation mark). Within the parameter file, the possibly titration
states of various individual residues may be defined. The syntax for
defining a titratable residue is:
RESI <resname> <nstate> ! nstate is the number of possible titration states.
RFPK <float> [<float>] ! reference pKa, of model compound
RFDG <float> [<float>] ! See notes section.
ATOM <type> <charge at state 1> <charge at state 2> [<charge at state 3>]
The file must end with "END" on a line by itself.
The parameter file containing the values used in the reference work may be
found in the support/parameters directory of the CHARMM distribution. Its name is
ph_param.prm.
Command syntax:
I/O:
READ CPH CARD UNIT <int> ! Read constant pH parameter file.
Defining titratable groups:
CNSPh {ADD [atom-selection]}
{DEL [atom-selection]}
{CLEAr }
ADD -- Any residue returned by the selection is added to the list
of titratable residues.
DEL -- Any residue returned by the selection is removed from the
list of titratable residues, if present.
CLEAr -- The list of titratable residues is emptied.
Running dynamics with constant pH:
DYNAmics ... PHCONS consph-spec
consph-spec::= PHEXCF <int> PHMCTR <int> [PHUNUM <int>] PHVAL <real>
[ IUNPHR <int> ] [ IUNPHw <int> ] [ PHTEMP <real> ]
[ IPHRSV <int> ]
keyword explanation
------- -----------
PHEXCF Frequency at which to attempt to change the titration state
of the system. Every PHEXCF steps, the dynamics will be
interrupted and the monte carlo procedure run.
PHMCTR The number of Monte Carlo trials to run. As of the current
implementation, the code picks a random residue of those
marked titratable to modify at each step.
PHUNUM The unit to write the current state of the system to at
each step. The syntax of the resulting file is given below.
The default is to not write any file.
PHVAL The pH value at which the simulation is performed.
PHTEMP Temperature to use in the pH exchange equation. If left
unset or if the value given is less than 0, the instantaneous
temperature of the system is used.
IUNPHR Unit to read a restart file from for use with constant pH (NB
the restart file for constant pH is kept separately from the
dynamics restart file).
IUNPHW Unit to write a restart file to for use with constant pH.
IPHRSV Writes a constant pH reservoir file to the specified unit number
for later use with pH reservoir replica exchange (see
repdstr.info for details). An entry will be written every
NSAVC time steps. Note this is only implemented for the
verlet and leapfrog verlet integrators.
Parameter file syntax:
The Constant pH parameter file follows regular CHARMM syntax conventions
(i.e. it must start with a title, and comment lines must begin with an
exclamation mark). Within the parameter file, the possibly titration
states of various individual residues may be defined. The syntax for
defining a titratable residue is:
RESI <resname> <nstate> ! nstate is the number of possible titration states.
RFPK <float> [<float>] ! reference pKa, of model compound
RFDG <float> [<float>] ! See notes section.
ATOM <type> <charge at state 1> <charge at state 2> [<charge at state 3>]
The file must end with "END" on a line by itself.
The parameter file containing the values used in the reference work may be
found in the support/parameters directory of the CHARMM distribution. Its name is
ph_param.prm.
Top
In the current implementation, each titratable residue can have at most
three different protonation states, of which only one is considered
"protonated." This is to accommodate Histidine, which has two different
deprotonated states. The first state listed in the parameter file should
be the fully protonated state (this is not enforced by the code, but is
how the equations are written).
The format of the PHUNUM state file is as follows for a system with N
titratable groups:
<timestep>: <group 1 start>-><group 1 end> ... <group N start>-><group N end>
At each timestep where a pH Monte Carlo trial is done, a new line is
appended to the file showing the starting and ending state of each titratable
group, separated by "->". The states are numbered, from one, in the order
that they appear in the parameter file. The residues appear in numerical
order (i.e. the first titratable residue by number will appear first, etc.).
Note that if a Monte Carlo trial is skipped at a particular time step due
to the use of pH replica exchange, no corresponding line will be added
to the PHUNUM file.
In order to protonate or deprotonate a residue, the charges on the
individual atoms are changed according to the charge values given in
the constant pH parameter file. Currently, no parameters other than the
charges are modified. Future work will expand this scheme to also modify
the van der Waal radii. Because of the way that this is implemented,
it is important that the PSF contain entries for all atoms. For this
reason, we suggest starting each simulation with all residues whose
titrations may change fully protonated.
Creating constant pH parameters:
The syntax of the parameter file is described above. Residues may
have two states or three states. If there are three states, only
the first one can be considered protonated; the other two are deprotonated.
If there are three states then two RFPK and RFDG values must be given.
The RFPK value(s) correspond to pKa,w and the RFDG value(s) correspond
to delta(Fele,w) in equation 1 of Itoh et al. (see reference). The
latter is the electrostatic component of the free energy differences
between the protonated and deprotonated states of the model compound.
This value can be obtained from free energy perturbation simulations
(» pert for details) or by running pH replica exchange at
different values until thew correct titration curve is achieved.
In the current implementation, each titratable residue can have at most
three different protonation states, of which only one is considered
"protonated." This is to accommodate Histidine, which has two different
deprotonated states. The first state listed in the parameter file should
be the fully protonated state (this is not enforced by the code, but is
how the equations are written).
The format of the PHUNUM state file is as follows for a system with N
titratable groups:
<timestep>: <group 1 start>-><group 1 end> ... <group N start>-><group N end>
At each timestep where a pH Monte Carlo trial is done, a new line is
appended to the file showing the starting and ending state of each titratable
group, separated by "->". The states are numbered, from one, in the order
that they appear in the parameter file. The residues appear in numerical
order (i.e. the first titratable residue by number will appear first, etc.).
Note that if a Monte Carlo trial is skipped at a particular time step due
to the use of pH replica exchange, no corresponding line will be added
to the PHUNUM file.
In order to protonate or deprotonate a residue, the charges on the
individual atoms are changed according to the charge values given in
the constant pH parameter file. Currently, no parameters other than the
charges are modified. Future work will expand this scheme to also modify
the van der Waal radii. Because of the way that this is implemented,
it is important that the PSF contain entries for all atoms. For this
reason, we suggest starting each simulation with all residues whose
titrations may change fully protonated.
Creating constant pH parameters:
The syntax of the parameter file is described above. Residues may
have two states or three states. If there are three states, only
the first one can be considered protonated; the other two are deprotonated.
If there are three states then two RFPK and RFDG values must be given.
The RFPK value(s) correspond to pKa,w and the RFDG value(s) correspond
to delta(Fele,w) in equation 1 of Itoh et al. (see reference). The
latter is the electrostatic component of the free energy differences
between the protonated and deprotonated states of the model compound.
This value can be obtained from free energy perturbation simulations
(» pert for details) or by running pH replica exchange at
different values until thew correct titration curve is achieved.