CV System

CudaSPONGE CV system documentation for SPONGE 1.4.

This page was translated by GPT-5.5 AI.

Input Control

Input commands are read through cv_in_file. The CV system consists of four parts: CV definitions, virtual atom definitions, CV usage, and program system control. For details, see File Formats. For the type notation used for each parameter, see Input Commands.

Virtual Atom Definitions

When calculating CVs, it is sometimes preferable to use virtual atoms instead of directly using the positions of multiple atoms. The positions of these virtual atoms are generated from other atoms.

center_of_mass

Center of mass

Parameters:

atom ([int]): atom list
atom_in_file (file): atom list file

center

Center calculated with arbitrary weights

Parameters:

atom ([int]): atom list
atom_in_file (file): atom list file
weight ([float]): weights
weight_in_file: weight file

CV Definitions

position_x

x coordinate

Parameters:

atom (int): atom

position_y

y coordinate

Parameters:

atom (int): atom

position_z

z coordinate

Parameters:

atom (int): atom

scaled_position_x

x coordinate divided by the box length along the x axis

Parameters:

atom (int): atom

scaled_position_y

y coordinate divided by the box length along the y axis

Parameters:

atom (int): atom

scaled_position_z

z coordinate divided by the box length along the z axis

Parameters:

atom (int): atom

box_length_x

Box length along the x axis

box_length_y

Box length along the y axis

box_length_z

Box length along the z axis

distance

Distance between two atoms

Parameters:

atom (int int): two atoms

displacement_x

x component of the displacement between two atoms

Parameters:

atom (int int): two atoms

displacement_y

y component of the displacement between two atoms

Parameters:

atom (int int): two atoms

displacement_z

z component of the displacement between two atoms

Parameters:

atom (int int): two atoms

angle

Angle formed by three atoms

Parameters:

atom (int int int): three atoms

dihedral

Dihedral angle formed by four atoms

Parameters:

atom (int int int int): four atoms

rmsd

RMSD between a series of atoms and the reference coordinates

The atom list and reference coordinates can be generated with Xponge maskgen.

Parameters:

atom ([int]): atom list
atom_in_file (file): atom list file
coordinate ([float]): reference coordinates
coordinate_in_file (float): reference coordinate file

combination

A value obtained by freely combining CVs Example:

                lx
        {
            CV_type = box_length_x
        }
        ly
        {
            CV_type = box_length_y
        }
        lz
        {
            CV_type = box_length_z
        }
        example_CV
        {
            CV_type = combination
            CV = lx ly lz
            function = lx * ly * lz
        }

In combination expressions, if floating-point numbers are involved, it is best to append f to indicate single-precision floating point, for example 1.0f. Using an integer where a floating-point number is expected may cause a just-in-time compilation error.

Parameters:

CV ([CV]): CVs to be combined

function ([string]): functional form used for the combination Supported functions and symbols:

Function	Symbol	Function	Symbol
a plus b	a + b	a minus b	a - b
a times b	a * b	a divided by b	a / b
a to the power of b	powf(a)(b)	natural logarithm of a	logf(a)
e to the power of a	expf(a)	complementary error function of a	erfcf(a)
square root of a	sqrtf(a)	cosine of a	cosf(a)
sine of a	sinf(a)	tangent of a	tanf(a)
arccosine of a	acosf(a)	arcsine of a	asinf(a)
arctangent of a	atanf(a)	absolute value of a	fabsf(a)
larger of a and b	fmaxf(a)(b)	smaller of a and b	fminf(a)(b)

tabulated

Tabulated mapping for a CV. Intermediate values are calculated with fourth-order B-spline interpolation. Example:

        lx
        {
            CV_type = box_length_x
        }
        example_CV
        {
            CV_type = tabulated
            CV = lx
            min = 0
            max = 100
            parameter = 1 4 0.2 7 9.1 -11
            min_padding = 1.1
            max_padding = 7.7
        }

This example corresponds to the following table: -60 | -40 | -20 | 0 | 20 | 40 | 60 | 80 | 100 | 120 | 140 | 160 --- | 1.1 | 1.1 | 1.1 | 1.0 | 4.0 | 0.2 | 7.0 | 9.1 | -11.0 | 7.7 | 7.7 | 7.7

Parameters:

CV ([CV]): CV to interpolate
min (float): minimum CV value
max (float): maximum CV value
parameter ([float]): list of mapped values
parameter_in_file (file): mapped value list file
min_padding (float): padding value used when the value is smaller than the minimum; used only for interpolation
max_padding (float): padding value used when the value is larger than the maximum; used only for interpolation

CV Usage

print

Print CVs Parameters:

CV ([CV]): CVs to print

restrain

Harmonic bias potential

U_{\rm bias} = \sum_{CV}{\rm weight} * (CV - {\rm reference})^2

The weight can change dynamically.

If start_step and max_step are not 0, while reduce_step and stop_step are 0, the weight has the following form:

           harmonic oscillator weight
                ^
          weight|         +-------------
                |        /
                |       /
                |      /
                0-----+---+------------>simulation steps
                   start max

If start_step and max_ste are 0, while reduce_step and stop_step are not 0, the weight has the following form:

           harmonic oscillator weight
                ^
          weight|----------------+
                |                 \
                |                  \
                |                   \
                0---------------+----+-->simulation steps
                             reduce stop

If all four step parameters are not 0, the weight has the following form:

           harmonic oscillator weight
                ^
          weight|         +------+
                |        /        \
                |       /          \
                |      /            \
                0-----+---+-----+----+-->simulation steps
                   start max reduce stop

Parameters:

CV ([CV]): CVs to restrain
weight ([float]): weights
reference ([float]): reference values
period ([float]): CV periods
start_step ([int]): step at which weight starts to increase linearly
max_step ([int]): step at which weight reaches its maximum
reduce_step ([int]): step at which weight starts to decrease linearly
stop_step ([int]): step at which weight becomes 0

steer

Linear bias potential

U_{\rm bias} = \sum_{CV} {\rm weight} * CV

Parameters:

CV ([CV]): CVs to which the bias potential is added
weight ([float]): weights

meta1d

One-dimensional metadynamics bias potential

U_{\rm bias} = \sum_t {\rm height} * N(CV_t, {\rm sigma}) * \text{welltemp factor}

Parameters:

CV (CV): CV to which the bias potential is added
CV_minimal (float): minimum CV value
CV_maximum (float): maximum CV value
dCV (float): grid spacing used when plotting the grid
potential_in_file (file): input file for the gridded CV potential energy curve
CV_period (float): CV period
height (float): height of the added Gaussian potential
sigma (float): standard deviation of the added Gaussian potential
wall_height (float): initial well depth when the CV is between the minimum and maximum values
welltemp_factor (float): welltemp factor; the smaller the value, the more slowly the Gaussian potential is added over time
potential_update_interval (int): interval between potential updates