mmpt (c38b1)
Molecular Mechanics with Proton Transfer (MMPT)
by Sven Lammers
and Jing Huang (jing.huang@unibas.ch)
and Markus Meuwly (m.meuwly@unibas.ch)
Questions and comments regarding MMPT should be directed to
----------------------------------------------------------
Jing Huang (jing.huang@unibas.ch)
Reference: S. Lammers, S. Lutz and M. Meuwly, J. Comp. Chem., 29,
1048 (2008)
The MMPT module contains reactive force fields to investigate proton
transfer (PT) reactions in MD simulations. It uses parametrized
three-dimensional potential energy surfaces (PESs) to describe
the interactions within a general DH--A proton transfer motif
where D is the donor, H is the hydrogen and A is the acceptor
atom. Together with the standard CHARMM force field and specific
rules control how bonded interactions on the donor and acceptor side
are switched on and off depending on the position of the transfering
H-atom (DH--A or D--HA). Multiple PT motifs can be located.
* Syntax | SYNTAX OF MMPT COMMAND
* Input files | MMPT INPUT FILES
* Limitations | LIMITATIONS
by Sven Lammers
and Jing Huang (jing.huang@unibas.ch)
and Markus Meuwly (m.meuwly@unibas.ch)
Questions and comments regarding MMPT should be directed to
----------------------------------------------------------
Jing Huang (jing.huang@unibas.ch)
Reference: S. Lammers, S. Lutz and M. Meuwly, J. Comp. Chem., 29,
1048 (2008)
The MMPT module contains reactive force fields to investigate proton
transfer (PT) reactions in MD simulations. It uses parametrized
three-dimensional potential energy surfaces (PESs) to describe
the interactions within a general DH--A proton transfer motif
where D is the donor, H is the hydrogen and A is the acceptor
atom. Together with the standard CHARMM force field and specific
rules control how bonded interactions on the donor and acceptor side
are switched on and off depending on the position of the transfering
H-atom (DH--A or D--HA). Multiple PT motifs can be located.
* Syntax | SYNTAX OF MMPT COMMAND
* Input files | MMPT INPUT FILES
* Limitations | LIMITATIONS
Top
Description of the MMPT command
The keyword MMPT should be used to invoke the MMPT module:
MMPT UHBR integer [USSM integer | USDM integer | UASM integer | -
UNLM integer | ULPE integer] [UHPM integer]
UHBR is the unit containing the list of proton transfer motifs. Each
motif is represented in one line using the following format:
-------------------------------------------------------------------
(PSF No. of D atom) (PSF No. of H atom) (PSF No. of A atom) (PES type)
-------------------------------------------------------------------
E.g. for protonated water dimer the file contains the following line:
1 7 4 SSM
There are five potential types currently supported, SSM (symmetric
single minimum), SDM (symmetric double minimum), ASM (asymmetric
single minimum), NLM (nonlinear hydrogen bond) and LPE (legendre
polynomials expansion). The detailed formula of these PESs can be
found in
- SSM, SDM and ASM:
S. Lammers, S. Lutz and M. Meuwly, J. Comp. Chem., 29, 1048 (2008)
- NLM:
Y. Yang and M. Meuwly, J. Chem. Phys., 133, 064503 (2010)
- LPE:
J. Huang, Ph.D. Thesis, University of Basel (2011)
For these PES types, the corresponding parameter files should be
provided in USSM, USDM, UASM, UNLM and ULPE, respectively. The
format is one parameter per line.
UHPM opens the unit containing the list of additional parameter for
angle and dihedral interactions on acceptor side atoms with transfered
hydrogen atom, in case that these newly formed angle or dihedral terms
are not given in the standard charmm parameter file. It should have
the following format:
---------------------------------------------------------
(No. of additional angle parameter)
(PSF No. of atom I) (PSF No. of atom J) (PSF No. of atom K)
(force constant) (equilibrium angle)
...
(No. of additional dihedral parameter)
(PSF No. of atom I) (PSF No. of atom J) (PSF No. of atom K)
(PSF No. of atom L) (force constant) (periodicity)
(equilibrium dihedral angle)
...
----------------------------------------------------------
E.g. in case of protonated diglyme, certain angle and dihedral
parameter have to be provided for the acceptor side.
The file contains the following line:
1
3 5 1 50.000 108.000
2
1 3 5 1 1.0000 3 180.000
3 3 5 1 1.0000 3 180.000
MMPT parameter files need to be opened on the units before MMPT is
called. It is suggested to invoke MMPT before any ENERgy,
MINImization, or DYNAmics command. It is also recommended to proceed
the MMPT command with an UPDAte so that non-bonded parameter lists
are up-to-date.
Description of the MMPT command
The keyword MMPT should be used to invoke the MMPT module:
MMPT UHBR integer [USSM integer | USDM integer | UASM integer | -
UNLM integer | ULPE integer] [UHPM integer]
UHBR is the unit containing the list of proton transfer motifs. Each
motif is represented in one line using the following format:
-------------------------------------------------------------------
(PSF No. of D atom) (PSF No. of H atom) (PSF No. of A atom) (PES type)
-------------------------------------------------------------------
E.g. for protonated water dimer the file contains the following line:
1 7 4 SSM
There are five potential types currently supported, SSM (symmetric
single minimum), SDM (symmetric double minimum), ASM (asymmetric
single minimum), NLM (nonlinear hydrogen bond) and LPE (legendre
polynomials expansion). The detailed formula of these PESs can be
found in
- SSM, SDM and ASM:
S. Lammers, S. Lutz and M. Meuwly, J. Comp. Chem., 29, 1048 (2008)
- NLM:
Y. Yang and M. Meuwly, J. Chem. Phys., 133, 064503 (2010)
- LPE:
J. Huang, Ph.D. Thesis, University of Basel (2011)
For these PES types, the corresponding parameter files should be
provided in USSM, USDM, UASM, UNLM and ULPE, respectively. The
format is one parameter per line.
UHPM opens the unit containing the list of additional parameter for
angle and dihedral interactions on acceptor side atoms with transfered
hydrogen atom, in case that these newly formed angle or dihedral terms
are not given in the standard charmm parameter file. It should have
the following format:
---------------------------------------------------------
(No. of additional angle parameter)
(PSF No. of atom I) (PSF No. of atom J) (PSF No. of atom K)
(force constant) (equilibrium angle)
...
(No. of additional dihedral parameter)
(PSF No. of atom I) (PSF No. of atom J) (PSF No. of atom K)
(PSF No. of atom L) (force constant) (periodicity)
(equilibrium dihedral angle)
...
----------------------------------------------------------
E.g. in case of protonated diglyme, certain angle and dihedral
parameter have to be provided for the acceptor side.
The file contains the following line:
1
3 5 1 50.000 108.000
2
1 3 5 1 1.0000 3 180.000
3 3 5 1 1.0000 3 180.000
MMPT parameter files need to be opened on the units before MMPT is
called. It is suggested to invoke MMPT before any ENERgy,
MINImization, or DYNAmics command. It is also recommended to proceed
the MMPT command with an UPDAte so that non-bonded parameter lists
are up-to-date.
Top
Explanation of input and output of MMPT
A typical input sequence for a MMPT simulation of protonated
water dimer looks as follows:
! OPEN PARAMETER FILES FOR HYDROGEN BONDS
OPEN UNIT 13 CARD READ NAME mmpt_ssm_o2h5p.prm
! OPEN FILE OF ATOMS WHICH FORM HYDROGEN BONDS
OPEN UNIT 14 FORMATTED READ NAME HBRIDGE.DAT
! RUN AN UPDATE TO INITIALISE NONBONDED ATOM PAIRS
UPDATE
! CALL MMPT ROUTINE, READ IN DATA
MMPT USSM 13 UHBR 14
CLOSE UNIT 13
CLOSE UNIT 14
Once MMPT is called, it first prints out the proton transfer motifs
that are treated by MMPT force field and then returns the information
that identifies the necessary modifications in the energy terms on
the donor and acceptor side:
MMPT> FOUND 1 HYDROGEN BOND(S) IN FILE:
MMPT> 1 7 4 SSM
MMPT> ENERGIES AND FORCES OF FOLLOWING
INTERACTIONS WILL BE REMOVED OR MODIFIED
BONDED TERMS: FLAG 1 MEANS TERM EXISTS
FLAG -1 MEANS TERM IS NEW
BONDS:
NO ATOM I ATOM J
5 1 O1 7 H5
ANGLES:
NO ATOM I ATOM J ATOM K FLAG
2 2 H1 1 O1 7 H5 1
3 3 H2 1 O1 7 H5 1
4 5 H3 4 O2 7 H5 -1
4 6 H4 4 O2 7 H5 -1
DIHEDRALS:
NO ATOM I ATOM J ATOM K ATOM L FLAG
IMPROPERS:
NO ATOM I ATOM J ATOM K ATOM L FLAG
NONBONDED TERMS: FLAG 1 MEANS TERM IS NEW
FLAG -1 MEANS TERM EXISTS
SPECIAL 1-4 VDW: FLAG 14 MEANS TERM IS NEW
SPECIAL 1-4 VDW: FLAG -14 MEANS TERM EXISTS
NONBONDED:
NO ATOM I ATOM J FLAG
1 4 O2 7 H5 0
2 1 O1 4 O2 0
3 2 H1 7 H5 -1
4 3 H2 7 H5 -1
5 5 H3 7 H5 1
6 6 H4 7 H5 1
The list contains the bond term of the donor acceptor which energy and
force is removed, two existing angle terms on the donor side which
are modified, and two new angle terms on the acceptor side which are
added, according to a switch function that turns the contributions on
and off depending on the position of the transferred proton.
Explanation of input and output of MMPT
A typical input sequence for a MMPT simulation of protonated
water dimer looks as follows:
! OPEN PARAMETER FILES FOR HYDROGEN BONDS
OPEN UNIT 13 CARD READ NAME mmpt_ssm_o2h5p.prm
! OPEN FILE OF ATOMS WHICH FORM HYDROGEN BONDS
OPEN UNIT 14 FORMATTED READ NAME HBRIDGE.DAT
! RUN AN UPDATE TO INITIALISE NONBONDED ATOM PAIRS
UPDATE
! CALL MMPT ROUTINE, READ IN DATA
MMPT USSM 13 UHBR 14
CLOSE UNIT 13
CLOSE UNIT 14
Once MMPT is called, it first prints out the proton transfer motifs
that are treated by MMPT force field and then returns the information
that identifies the necessary modifications in the energy terms on
the donor and acceptor side:
MMPT> FOUND 1 HYDROGEN BOND(S) IN FILE:
MMPT> 1 7 4 SSM
MMPT> ENERGIES AND FORCES OF FOLLOWING
INTERACTIONS WILL BE REMOVED OR MODIFIED
BONDED TERMS: FLAG 1 MEANS TERM EXISTS
FLAG -1 MEANS TERM IS NEW
BONDS:
NO ATOM I ATOM J
5 1 O1 7 H5
ANGLES:
NO ATOM I ATOM J ATOM K FLAG
2 2 H1 1 O1 7 H5 1
3 3 H2 1 O1 7 H5 1
4 5 H3 4 O2 7 H5 -1
4 6 H4 4 O2 7 H5 -1
DIHEDRALS:
NO ATOM I ATOM J ATOM K ATOM L FLAG
IMPROPERS:
NO ATOM I ATOM J ATOM K ATOM L FLAG
NONBONDED TERMS: FLAG 1 MEANS TERM IS NEW
FLAG -1 MEANS TERM EXISTS
SPECIAL 1-4 VDW: FLAG 14 MEANS TERM IS NEW
SPECIAL 1-4 VDW: FLAG -14 MEANS TERM EXISTS
NONBONDED:
NO ATOM I ATOM J FLAG
1 4 O2 7 H5 0
2 1 O1 4 O2 0
3 2 H1 7 H5 -1
4 3 H2 7 H5 -1
5 5 H3 7 H5 1
6 6 H4 7 H5 1
The list contains the bond term of the donor acceptor which energy and
force is removed, two existing angle terms on the donor side which
are modified, and two new angle terms on the acceptor side which are
added, according to a switch function that turns the contributions on
and off depending on the position of the transferred proton.
Top
Limitations of current MMPT module
Continuous proton transfer, e.g. proton shuttling along a water chain, is
not possible with current MMPT module. A new version that allows proton
transport is under development.
The maximum number of MMPT motifs is 200. This can be increased by
changing the variable NHBNUM in the subroutine ALLOCFIR if needed.
Limitations of current MMPT module
Continuous proton transfer, e.g. proton shuttling along a water chain, is
not possible with current MMPT module. A new version that allows proton
transport is under development.
The maximum number of MMPT motifs is 200. This can be increased by
changing the variable NHBNUM in the subroutine ALLOCFIR if needed.