Interface to dynamics codes¶
Description¶
BAGEL can be used for performing QM/MM calculations and direct dynamics simulations, by interfacing it to external software. The “electrostatic embedding” scheme is used in inserting the QM region in MM region. BAGEL exports the gradients of the energy with respect to the displacements of the QM particles and MM particles in a form that can be directly read by the dynamics codes.
How It Works¶
The communications between the quantum chemistry codes and the molecular dynamics codes are based on the text files. For example, in molecular dynamics (MD) jobs, after the trajectory initiates, the positions of the QM atoms and MM particles, and the charges of MM particles are passed into BAGEL, in a form of text input. The quantum chemical calculation is performed to calculate any needed quantities (such as energies, its gradients, and NACMEs for nonadiabatic dynamics). This is passed (exported) to the form that can be read by the dynamics program, and the dynamics program propagates the trajectory according to these gradients. After a one time integration step, the positions of QM atoms and MM particles are again passed into BAGEL. This continues until the trajectory integration ends.
In summary, to perform the dynamics simulations with external programs one needs:
quantum chemistry input writer in the dynamics program
quantum chemistry information output writer in the quantum chemistry program
quantum chemistry output parser in the dynamics program
is included in BAGEL (with a keyword of
exportandexport_single); the users should insert (1) and (3) in the dynamics code.
Input Format¶
The BAGEL input for QM/MM jobs is same to that used in the quantum chemistry, except for the external charges. The external MM charge can be added in BAGEL calculation, as
{ "atom" : "Q", "xyz" : [ %lf, %lf, %lf ], "charge" : %lf }
where xyz has the positions, and charge has the charge on the MM particle (in the units of e).
Export Format¶
Some of dynamics software reads the informations in a fixed form. The gradient export format is as follows.
The name of the file exported is ENERGY.txt (energy), FORCE_%d.txt (gradient, %d is the number of the state)
and NACME_%d_%d.txt (derivative coupling). The gradient is written in FORCE.txt when export_single is true.
0 1 2
%6d %20.10lf %20.10lf %20.10lf
//(atomno) (X component) (Y component) (Z component)
Note that the QM and MM atoms is not distinguished to each other in the exported output. The exported gradients and nonadiabatic couplings are in the units of Hartrees/bohr and 1/bohr. The energy is also exported, as
%20.10lf
// (statewise energy)
The energies for the multiple states in ascending order are exported in the same file when one does multi-state calculations, such as SA-CASSCF and XMS-CASPT2.
Files to be Modified in Dynamics Software¶
Some source codes in the dynamics software should be modified. Many of the dynamics software in fact have QM/MM
interfaces to the other quantum chemistry software, and by modifying the existent interface, one can perform the
QM/MM dynamics or gas phase dynamics simulations. For instance, to perform QM/MM calculations in GROMACS, one should modify
src/gromacs/mdlib/qmmm.c,
add a BAGEL interface code to
src/gromacs/mdlib/qm_bagel.c.
This should contain the code for writing appropriately formatted input for BAGEL. Additionally, include BAGEL for QM package for QM/MM in the CMake installation option in
CMakeLists.txt
(as of version 5.1.4).
Keywords¶
export
true: Export filefalse: Do not export filetrue.export_single
true: Export filefalse: Do not export filetrue with single state dynamics / optimizations.Example¶
Sample input¶
A sample input for HF molecule using CASSCF. This input computes the nuclear gradient for states 0 and 1 as well as the derivative coupling vector between these two states:
{ "bagel" : [
{
"title" : "molecule",
"basis" : "svp",
"df_basis" : "svp-jkfit",
"angstrom" : false,
"geometry" : [
{ "atom" : "H", "xyz" : [ -0.000000, -0.000000, 1.700000] },
{ "atom" : "F", "xyz" : [ -0.000000, -0.000000, 0.000000] }
]
},
{
"title" : "forces",
"grads" : [
{ "title" : "force", "target" : 0 },
{ "title" : "force", "target" : 1 },
{ "title" : "nacme", "target" : 0, "target2" : 1 }
],
"export" : true,
"method" : [ {
"title" : "casscf",
"nopen" : 0,
"nact" : 2,
"nclosed" : 4,
"nstate" : 2
} ]
}
]}
Executing BAGEL with this input will generate the following text files:
ENERGY.out¶
-99.9135619715
-99.5339025461
FORCE_0.out¶
0 1 2
0 -0.0000000000 -0.0000000000 -0.0019342533
1 0.0000000000 0.0000000000 0.0019342533
FORCE_1.out¶
0 1 2
0 0.0000000000 0.0000000000 -0.2535235791
1 -0.0000000000 -0.0000000000 0.2535235791
NACME_0_1.out¶
0 1 2
0 -0.0355272749 -0.0991581135 0.0000000000
1 -0.0285426596 -0.0796637587 -0.0000000000