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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


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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.

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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---