Metadynamics Simulations

Parameters for Metadynamics

meta

The meta block is used to set up a metadynamics simulation. The block must include a definition of the collective variables (CVs), the Gaussian potential, the time range over which they are added, and the interval between addition. The metadynamics output file and the log file must also be defined. The parameters for this block are listed in Table 1.

Table 1. Parameters that apply to the entire metadynamics simulation

Parameter	Description
height	Height of the repulsive Gaussian potential, in kcal/mol.
first	Time in ps at which the Gaussian potentials are first added. Default: zero time.
last	Time in ps at which the Gaussian potentials are last added. Default: simulation time.
interval	Interval in ps at which the Gaussian potentials are subsequently added. A smaller interval means that Gaussians are added more frequently.
name	Name of the metadynamics output file. This file contains the Gaussian widths and height at each step, and is used to calculate the free energy.
cv_name	Name of the metadynamics log file. Default: $SJOBNAME.cvseq.
cv	Map that defines the collective variables—see cv.

An example is given below.

meta = {
  cv = {cv-map}
  cv_name = $JOBNAME.cvseq
  first = 0.0
  height = 0.03
  interval = 1.2
  name = kernels.kerseq
} 

Multisim also supports well-tempered metadynamics, through the meta.kTemp keyword, which specifies the value of kT. For more information on well-tempered metadynamics, see its sample pot file.

cv

The cv parameter defines the collective variables in a metadynamics simulation. Each variable is defined in a map that includes the type, the atom groups that are included in the collective variable, and the RMS width of the repulsive Gaussian potential. Atom groups are either a single atom or the center of mass of a list of atoms. For some variables, a wall (upper bound) or a floor (lower bound) can be placed at specified values of the variable, which prevents the system from moving too far in either direction defined by the collective variable. The parameters that can be used to define a collective variable are summarized in Table 2.The available collective variables are summarized in Table 3. Distance variables are in angstroms, angles are in degrees.

Table 2. Parameters for collective variables

Parameter	Description
type	Collective variable type. See Table 3 for a list of allowed types.
atom	Atom groups that define the group of a collective variable. The group can be a single atom or the center of mass of a list of atoms. The number of groups is given in Table 3 for each variable type.
width	RMS width of the repulsive Gaussian potential.
wall	Upper bound on the value of the collective variable. The system is prevented from making a step beyond this value.
floor	Lower bound on the value of the collective variable. The system is prevented from making a step beyond this value.
range	Range of values of the collective variable to be used in the analysis, defined as a list with a lower and an upper value.

 

Table 3. Collective variable types

type	Description	Default Width	Wall	Floor	Atom Groups
dist	Distance	0.05 Å	yes	yes	2
angle	Angle	2.5°	yes	yes	3
dihedral	Dihedral	5.0°	no	no	4
rgyr	Radius of gyration	0.1 Å	no	no	1
rgyr_mass	Mass-weighted radius of gyration	0.1 Å	no	no	1
rmsd	RMSD from aligned starting structure	0.1 Å	no	no	1
rmsd_symm	Symmetry aware RMSD	0.1 Å	no	no	1
zdist	Distance along the z axis	0.05 Å	yes	yes	1
zdist0	Absolute distance along the z axis	0.1 Å	yes	yes	1
whim1	WHIM1 - first principal moment [35]	0.5 Å2	no	no	1
whim2	WHIM2 - second principal moment [35]	0.25 Å2	no	no	1

For the analysis, the range of coordinate values can be defined, with the range parameter. This is useful if the interesting phenomena occur at the end of the range, e.g. at 180° for a dihedral angle. An example with two CVs is as follows:

cv = [ { type = dist
         atom = [1 3]
         width = 0.4
         wall = 10.0
 
       { type = angle
         atom = [1 3 5 6]
         width = 0.4
         range = [0 360] } ]

To define a collective variable in terms of the center of mass of a set of atoms, you can provide an ASL expression inside the atom list to define each atom site, e.g.

atom = [ "at.n 12-17" "at.n 19-21" ] 
type = "dist"

You can also use ASL to define the center of mass in a meta block in the .msj file. For more information on ASL, see Atom Specification Language.

 simulate {
   cfg_file = "config.cfg"
   jobname = "$MAINJOBNAME"
   dir = "."
   compress = ""
   meta = {
     cv = [
       {atom = ["mol.n 2 and not a.e H"]
        type = "rgyr"
        width = 0.15
       }
       {atom = ["(res.num 124 and protein) and not a.e H" "mol.num 2 and not a.e H"]
        type = "dist"
        width = 0.05
       }
     ]
     cv_name = "$JOBNAME$[_replica$REPLICA$].cvseq"
     first = 0.0
     height = 0.03
     interval = 0.03
     name = "$JOBNAME$[_replica$REPLICA$].kerseq"
   }
   checkpt.write_last_step = yes
 }