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mndo97

Combined Quantum Mechanical and Molecular Mechanics Method Based on MNDO97 in CHARMM by Paul Bash (pabash@nwu.edu) Additional modifications Kwangho Nam(nam@chem.umn.edu) and Darrin York * Description / Description of the MNDO97 commands * Usage / How to run MNDO97 in CHARMM * NEWD / NEWD Command * Installation / How to install MNDO97 in CHARMM environment
Top The MNDO97 QM potential is initialized with the MNDO97 command. [SYNTAX MNDO97] MNDO97 [REMOve] [EXGRoup] (atom selection) [GLNK atom-selection] [AM1|PM3|MNDO|MNDD|AMDD] [PHOT] [CHARge int] [SWITched] [DXLBomd] [NORDder int] [NSTEpscf int] [NEWD int] ewald-spec [NOPMewald] ewald-spec::= { [ KMAX integer ] } KSQMAX integer { KMXX integer KMXY integer KMXZ integer } REMOve: Classical energies within QM atoms are removed. EXGRoup: QM/MM Electrostatics for link host groups removed. GLNK: GHO method implementation (refer qmmm.doc). AM1: The AM1 method is to be used. (default) PM3: The PM3 method is to be used. MNDO: The MNDO method to be used. MNDD: The MNDO/d method to be used. AMDD: The AM1/d method to be used. (This method has very limited number of atoms supported. Specifically, use in combination with PHOT keyword.) PHOT: For the AM1/d method, PHOT use the AM1/d-PhoT method (Nam, JCTC, 2007). Also, for Mg atom, it uses AM1 parameters. CHARge: Total charge of QM region. (At present, it only supports RHF options.) SWITched: Use the (group-based) switching function for the QM-MM interactions. See below, if this option is used together with QM/MM-Ewald or QM/MM-PME method. DXLBomd: This uses the Niklasson JCP (2009) 130:214109 and Zheng JCT (2011) 135:044122, in which the quess QM density is propagated using Dissipated Lagrandian MD. The dissipation requires user to provide two variables. They are provided using NORDder : The maximum order to sum the dissipation terms. At present, only terms between 3 and 9 are supported. See Niklasson JCP (2009) 130:214109. NSTEpscf: The number of SCF cycle. Mostly, 7 or larger is safe. Also, in many cases smaller than 7 SCF cycles provides stable MD simulations. For details of the method, please refer Niklasson JCP (2009) 130:214109 and Zheng JCT (2011) 135:044122. Current implementation has a limit in choosing non-bonded options. All atom based cutoffs methods is not fully supported for a certain boundary conditions such as periodic boundary condition. In any case, the QM-MM non-bond generation routine will only generate the non-bond list based on group-group separation scheme. Especially to use any periodic boundary conditions, use group based cutoff scheme.
Top Description of the NEWE Command [ NEWD int ] ewald-spec [NOPMewald] ewald-spec::= { [ KMAX integer ] } KSQMAX integer { KMXX integer KMXY integer KMXZ integer } A simple Ewald sum method is implemented into the QM/MM potential. A full description of theory is described in J. Chem. Theory. Comput. (2005) 1, 2 and Nam. JCTC (2014). With NOPMewald, the regaular Ewald sum method is used for the QM/MM calculation. So, this option is denoted as QM/MM-Ewald method. Without NOPMewald, if the MM use PME method, the QM/MM part is also QM/MM-PME method. (see ewald.doc). The defaults for the QM/MM-Ewald calculations are set internally and are currently set to NEWD 1, KMAX=5, KSQMax=27, where the KMAX keyword is the number of kvectors (or images of the primary unit cell) that will be summed in any direction. It is the radius of the Ewald summation. For orthorombic cells, the value of kmax may be independently specified in the x, y, and z directions with the keywords KMXX, KMXY, and KMXZ. But, different from regular Ewald in CHARMM, it has no limitation on the shape of box, and can be used with PMEwald in MM part. The KSQMax key word should be chosen between KMAX squared and 3 times KMAX squared, and KAPPA value share the exact same number you use in Nonbond options. When QM/MM-Ewald or QM/MM-PME method is used together with the SWITched option. The total energy is expressed as E_total = Sw(r)*E_qm/mm(real space) + dE_qm/mm(periodic correction) + E_mm E_qm/mm(real space): The regular QM/MM interaction, in which MM point charges interact with the entire QM (electron) density. dE_qm/mm(periodic correction) = (1-Sw(r))*dE_qm/mm (real space part) + dE_qm/mm(reciprocal space part) where d= Dela. For each term, refer Nam JCTC (2005) 1, 2, and Nam JCTC (2014) 10, 4175. When this is used with the SWITched option, the real space is switched off at the cutoff distance, and dE_qm/mm (real space part) is turned on slowly between the cut on and cut off distances. This makes the transition from the full QM/MM real space potential to the dE_qm/mm (real space part) correction smoothly and thus generate more stable MD trajectory.
Top MNDO97/CHARMM interface status (February 1997) - MNDO97, CADPAC, GAMESS and QUANTUM keywords cannot coexist in pref.dat To compile MNDO97 with CHARMM one uses: install.com [machine] [size] W The "W" specifies to compile and link MNDO97 with CHARMM.