msmmpt (c47b2)
Multi-state Molecular Mechanics with Proton Transfer (MS-MMPT)
by Zhen-Hao Xu (zhexu@uni-mainz.de)
and Markus Meuwly (m.meuwly@unibas.ch)
Questions and comments regarding MS-MMPT should be directed to
----------------------------------------------------------
Zhen-Hao Xu (z.xu@unibas.ch)
Reference: Z.-H. Xu and M. Meuwly, J. Phys. Chem. B (2019) in print
MS-MMPT has been developed, based on the established MMPT module, to
investigate diffusive proton transport in the condensed phase. The
MS-MMPT module extends the MMPT force field with multi-surface adiabatic
reactive molecular dynamics (MS-ARMD) to describe multiple proton binding
motifs. In the MS-MMPT method, a global potential energy for proton
transport is built by mixing multiple bonding patterns of a proton bonded
to a possible acceptor atom. This method has been applied to proton
diffusion in water clusters and in bulk.
Notes for users:
1. MS-MMPT combines MMPT with MS-ARMD module. For the introduction and
usage of MMPT force field, please consult mmpt.doc
2. The current implementation of MS-MMPT is geared towards the dynamics
of the excess proton in water.
3. Treating multiple excess protons has not been validated.
4. MS-MMPT supports the symmetric single (SSM), symmetric double (SDM),
nonlinear minimum (NLM) potentials and the potential with Legendre
polynomial expansion (LPE) from MMPT.
* Syntax | SYNTAX OF MSMMPT COMMAND
* Input files | MSMMPT INPUT FILES
by Zhen-Hao Xu (zhexu@uni-mainz.de)
and Markus Meuwly (m.meuwly@unibas.ch)
Questions and comments regarding MS-MMPT should be directed to
----------------------------------------------------------
Zhen-Hao Xu (z.xu@unibas.ch)
Reference: Z.-H. Xu and M. Meuwly, J. Phys. Chem. B (2019) in print
MS-MMPT has been developed, based on the established MMPT module, to
investigate diffusive proton transport in the condensed phase. The
MS-MMPT module extends the MMPT force field with multi-surface adiabatic
reactive molecular dynamics (MS-ARMD) to describe multiple proton binding
motifs. In the MS-MMPT method, a global potential energy for proton
transport is built by mixing multiple bonding patterns of a proton bonded
to a possible acceptor atom. This method has been applied to proton
diffusion in water clusters and in bulk.
Notes for users:
1. MS-MMPT combines MMPT with MS-ARMD module. For the introduction and
usage of MMPT force field, please consult mmpt.doc
2. The current implementation of MS-MMPT is geared towards the dynamics
of the excess proton in water.
3. Treating multiple excess protons has not been validated.
4. MS-MMPT supports the symmetric single (SSM), symmetric double (SDM),
nonlinear minimum (NLM) potentials and the potential with Legendre
polynomial expansion (LPE) from MMPT.
* Syntax | SYNTAX OF MSMMPT COMMAND
* Input files | MSMMPT INPUT FILES
Top
Description of the MSMMPT command
The keyword MSPT should be used to invoke the MS-MMPT module:
MSPT UHBR integer [USSM integer | USDM integer | UNLM integer -
| ULPE integer ] UMUL integer
UHBR is the unit containing the list of initial proton transfer motifs.
The 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 NLM
‘D’ is the donor atom, ‘A’ is the acceptor atom.
The type of proton transfer potential should be chosen from one of the
following:
USSM is the unit representing for a PT potential with a single minimum
USDM is the unit representing for a PT potential with symmetric double minimum
UNLM is the unit representing for a PT potential with a non-linear path
ULPE is the unit representing for a PT potential which contains Legendre
polynomial expansion
UMUL is the unit reading necessary parameters for the MS-MMPT module.
Without specifying the UMUL unit, MS-MMPT will not be called.
!############################################################
! An input example of MS-MMPT parameter file with a
! X-D--H*--A-Y bond connection in which D--H*--A is a defined
! proton transfer motif
!############################################################
OPEN UNIT 15 CARD WRITE NAME msmmpt_wat.prm
WRITE TITLE UNIT 15
* 5.0 ! delta_E
* 0.2213 ! force constant (fc) of the dihedral term (X-D--A-Y)
* 10.985 ! fc of the supplementary angular terms (X-D--H* or H*--A-Y)
* 128.432 ! equilibrium (eq) of the supplementary angular terms
* 0.66 ! partial point charge of H* by definition
* 552.94 ! fc of OH bond in H3O+ representation (rep.)
* 0.9726 ! eq of OH bond in H3O+ rep., turn negative to deactivate the resonance struture for bonds
* 31.18 ! fc of HOH bend in H3O+ rep.
* 112.73 ! eq of HOH bend in H3O+ rep., turn negative to deactivate the resonance struture for angles
* 592.23 ! fc of OH bond in H2O force field (#)
* 0.9657 ! eq of OH bond in H2O (#)
* 59.26 ! fc of HOH bend in H2O (#)
* 106.56 ! eq of HOH bend in H2O (#)
* -0.198 ! EPSI_Oxy (H3O+), vdW parameters for H3O+ rep.
* 1.734 ! RMIN_Oxy (H3O+), a negative value deactivates resonance strutures for vdW
* -0.000 ! EPSI_Hyd (H3O+)
* 0.001 ! RMIN_Hyd (H3O+), a negative value deactivates resonance strutures for vdW
* -0.1554253 ! EPSI_Oxy (H2O), vdW parameters of H2O force field (#)
* 1.776572 ! RMIN_Oxy (H2O)
* -0.000 ! EPSI_Hyd (H2O)
* -99.00 ! RMIN_Hyd (H2O)
* -999.0 ! Length of a periodic box in X-dir. (#)
* -999.0 ! Length of a periodic box in Y-dir. (#)
* -999.0 ! Length of a periodic box in Z-dir. (#)
CLOSE UNIT 15
The special note (#) denotes the parameters given by CHARMM input or
topology files. If PBC is not called, specify with arbitrary negative values.
Description of the MSMMPT command
The keyword MSPT should be used to invoke the MS-MMPT module:
MSPT UHBR integer [USSM integer | USDM integer | UNLM integer -
| ULPE integer ] UMUL integer
UHBR is the unit containing the list of initial proton transfer motifs.
The 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 NLM
‘D’ is the donor atom, ‘A’ is the acceptor atom.
The type of proton transfer potential should be chosen from one of the
following:
USSM is the unit representing for a PT potential with a single minimum
USDM is the unit representing for a PT potential with symmetric double minimum
UNLM is the unit representing for a PT potential with a non-linear path
ULPE is the unit representing for a PT potential which contains Legendre
polynomial expansion
UMUL is the unit reading necessary parameters for the MS-MMPT module.
Without specifying the UMUL unit, MS-MMPT will not be called.
!############################################################
! An input example of MS-MMPT parameter file with a
! X-D--H*--A-Y bond connection in which D--H*--A is a defined
! proton transfer motif
!############################################################
OPEN UNIT 15 CARD WRITE NAME msmmpt_wat.prm
WRITE TITLE UNIT 15
* 5.0 ! delta_E
* 0.2213 ! force constant (fc) of the dihedral term (X-D--A-Y)
* 10.985 ! fc of the supplementary angular terms (X-D--H* or H*--A-Y)
* 128.432 ! equilibrium (eq) of the supplementary angular terms
* 0.66 ! partial point charge of H* by definition
* 552.94 ! fc of OH bond in H3O+ representation (rep.)
* 0.9726 ! eq of OH bond in H3O+ rep., turn negative to deactivate the resonance struture for bonds
* 31.18 ! fc of HOH bend in H3O+ rep.
* 112.73 ! eq of HOH bend in H3O+ rep., turn negative to deactivate the resonance struture for angles
* 592.23 ! fc of OH bond in H2O force field (#)
* 0.9657 ! eq of OH bond in H2O (#)
* 59.26 ! fc of HOH bend in H2O (#)
* 106.56 ! eq of HOH bend in H2O (#)
* -0.198 ! EPSI_Oxy (H3O+), vdW parameters for H3O+ rep.
* 1.734 ! RMIN_Oxy (H3O+), a negative value deactivates resonance strutures for vdW
* -0.000 ! EPSI_Hyd (H3O+)
* 0.001 ! RMIN_Hyd (H3O+), a negative value deactivates resonance strutures for vdW
* -0.1554253 ! EPSI_Oxy (H2O), vdW parameters of H2O force field (#)
* 1.776572 ! RMIN_Oxy (H2O)
* -0.000 ! EPSI_Hyd (H2O)
* -99.00 ! RMIN_Hyd (H2O)
* -999.0 ! Length of a periodic box in X-dir. (#)
* -999.0 ! Length of a periodic box in Y-dir. (#)
* -999.0 ! Length of a periodic box in Z-dir. (#)
CLOSE UNIT 15
The special note (#) denotes the parameters given by CHARMM input or
topology files. If PBC is not called, specify with arbitrary negative values.
Top
Explanation of input and output of MSMMPT
!############################################################
! A typical CHARMM input sequence for a MSMMPT simulation
! looks as follows:
!############################################################
! OPEN PARAMETER FILES FOR HYDROGEN BONDS
OPEN UNIT 13 CARD READ NAME mmpt_h5o2p.prm
! OPEN FILE OF ATOMS WHICH FORM HYDROGEN BONDS
OPEN UNIT 14 FORMATTED READ NAME hbridge.dat
! OPEN PARAMETER FILES FOR MS-MMPT MODULES
OPEN UNIT 15 CARD READ NAME msmmpt_wat.prm
! RUN AN UPDATE TO INITIALISE NONBONDED ATOM PAIRS
UPDATE
! CALL MMPT ROUTINE, READ IN DATA
MSPT UNLM 13 UHBR 14 UMUL 15
CLOSE UNIT 13
CLOSE UNIT 14
CLOSE UNIT 15
!---END---
Explanation of input and output of MSMMPT
!############################################################
! A typical CHARMM input sequence for a MSMMPT simulation
! looks as follows:
!############################################################
! OPEN PARAMETER FILES FOR HYDROGEN BONDS
OPEN UNIT 13 CARD READ NAME mmpt_h5o2p.prm
! OPEN FILE OF ATOMS WHICH FORM HYDROGEN BONDS
OPEN UNIT 14 FORMATTED READ NAME hbridge.dat
! OPEN PARAMETER FILES FOR MS-MMPT MODULES
OPEN UNIT 15 CARD READ NAME msmmpt_wat.prm
! RUN AN UPDATE TO INITIALISE NONBONDED ATOM PAIRS
UPDATE
! CALL MMPT ROUTINE, READ IN DATA
MSPT UNLM 13 UHBR 14 UMUL 15
CLOSE UNIT 13
CLOSE UNIT 14
CLOSE UNIT 15
!---END---