MBO(N)D

7       Methodology--Standalone Mode

Running an MBO(N)D simulation in standalone mode

Assuming that you have a properly prepared input script file named run_name.inp and an executable named mbond.exe, the simplest way to submit a run is to enter at the UNIX prompt:

>	/pathname/mbond.exe < run_name.inp > run_name.out &

#comments
#comments
#comments
/pathname/mbond.exe < $1.inp > $1.out

>	run.com run_name &

Other input files

The other input files for an MBO(N)D CHARMm simulation are:

• CHARMm RTF file.

• CHARMm parameter file.

• CHARMm PSF file (optional).

• CHARMm coordinate file in .crd or .pdb format.

• Stream (.str) file containing MBO(N)D substructuring information.

• Modes files for each flexible body defined in the .str file (optional).

• CHARMm .rst file (from an atomistic equilibration run, an MBO(N)D equilibration run, or an MBO(N)D production run; optional).

Substructured molecular dynamics is invoked by using the MBOND option of the regular CHARMm DYNAmics command. This enables several keywords particular to MBO(N)D and disables some that are not supported. In general, however, all the standard DYNAmics keywords are supported, unless specifically mentioned here.

See the CHARMm documentation for details on the DYNAmics command.

Bodies and modes

Bodies must have been defined prior to invoking MBO(N)D dynamics (see SUBStructure). If no modes have been loaded (or generated) for the bodies, they are assumed to be rigid.

Temperature control

Only velocity scaling is supported for heating and equilibration protocols. However, the initial velocities may be assigned using any of the CHARMm options (including using a restart file). The thermostat that is available is a simple Berendsen method.

Printing of the overall temperature and the temperature of the body and atomistic regions can be separately controlled by the TFRQ option in the DYNAmics command. In addition, this reports the individual kinetic energy of each body.

Simulation stages

A typical protocol is to heat a system using an atomistic simulation, then equilibrate it and generate modes. When the switch is made to a substructured simulation, the system needs to be equilibrated once more before the data-collection stage of dynamics can begin.

Multiple time scales

Multiple time scales are supported in MBO(N)D. As usual, the MTS keyword must precede dynamics simulation. The MASS and DISTANCE keywords must be specified. They segregate nonbond interaction updating by combined mass/distance criterion (Multiple time scales). You can specify the number of stages for the MTS via the ratios keyword or allow it to be computed automatically.

The following CHARMm features are not supported in multibody simulations: SHAKE constraints (although bond length constraints between bodies and particles are supported with the HINGE BOND command), constant-pressure dynamics, Nosé-Hoover temperature control, Langevin dynamics.

Integrators

The integrators that MBO(N)D does support are Lobatto and MTS Lobatto. The leapfrog and 4D Verlet algorithms cannot be used.

General outline of command input file

1. Read in the topology and parameter files.

2. Read in the CHARMm .psf (protein structure file), which contains the list of atoms in the system being simulated and their connectivities. Alternatively, generate the structure (and the .psf file) within CHARMm.

3. Read in the starting coordinates, either in the CHARMm .crd or .pdb formats (coordinates only) or from a CHARMm .rst file (restart file, which contains both coordinates and velocities).

4. Specify the desired substructuring for your MBO(N)D run.

5. If bodies are flexible, generate or load (from file) the mode shape vectors to be used for each body.

6. Initiate MBO(N)D dynamics simulation using the DYNAMICS MBOND command.

Control commands

• SET string1 string2--Define string1 as string2, exactly as it appears.

The SET command is helpful when files with long pathnames are used more than once. It is also useful for defining and resetting a a parameter that is used often in the script.

• bomlev #--Set the level of error severity that causes an MBO(N)D CHARMm job to terminate. # is usually set to -1.

• OPEN READ UNIT # FORM/UNFORM--Open a file of unit # for reading.

• READ RTF--Read a topology file.

• READ PARA--Read a parameter file.

• READ PSF--Read the CHARMm PSF file.

• READ COOR--Read a set of coordinates in CHARMm .crd format.

• STREAMfilename --Read in a file containing information that is used repeatedly over many runs, such as substructuring information.

• NBOND options--A CHARMm command that allows you to set various nonbond interaction options, such as options for the update of the nonbond interaction list and options that determine how the van der Waals and Coulombic interactions are evaluated. These options are described more fully in the CHARMm Dictionary (online).

• MBOND ATOM--Control how interactions within flexible bodies are computed. If MBOND ATOM is activated, the intrabody interactions are calculated using the CHARMm forcefield. If MBOND ATOM is not invoked, then the intrabody interactions are calculated using the modal stiffness terms associated with the modes.

• MBOND NBODY nb--Activate MBO(N)D to receive substructuring and modal information. nb is the number of bodies. (See also SUBStructure.)

• SUBSTRUCTURE--Identify collections of atoms to group into bodies (SUBStructure). Identify the body with the CHARMm SELECTION commands (see CHARMm Dictionary).

• MODES--Activate the MBO(N)D capability to read in modal information through mode files (MODES).

• LOAD--Load the information from the modal file (MODES).

• USEM--Given a number of modes loaded into the system, USEM allows you to use a subset of them (MODES).

• GENERATE--Calculate NMODE modes for the specified body.

• PED--The MBO(N)D version of the CHARMm facility to be used for analyzing body-based modes. Modes must have been already loaded and must be vacuum modes.

Dynamics commands

• DYNAMICS MBOND (RE)START--This command is analogous to the usual CHARMm command (see CHARMm Dictionary), except for the MBO(N)D keywords, which can be used to invoke the MBO(N)D dynamics program (see also DYNAMICS).

• LOBATTO--Invoke the Lobatto integrator.

• MTS--This command, when it appears within an MBOND block, invokes the MBO(N)D multiple time scale integrator.

• MBPRLEV--Determine the extent of MBO(N)D-relevant information printed out during the run. A value of -1 prints out the least information, and a value of 9 prints out the maximum amount of information. Use values above -1 only when debugging (see DYNAMICS).

• VECFRQ--Determine the frequency with which MBO(N)D vector information is output. As with MBPRLEV, a value different from 0 is used mainly for debugging purposes.

Output commands

• OPEN WRITE UNIT #--Open a file of unit # for writing.