CHARMM c42b2 mmpt.doc



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           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.


* Menu:

* Syntax::                SYNTAX OF MMPT COMMAND
* Input files::           MMPT INPUT FILES 
* Limitations::           LIMITATIONS



File: MMPT -=- Node: Syntax
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 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. 




File: MMPT -=- Node: Input Files
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 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.




File: MMPT -=- Node: Limitations
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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. 

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