CV:MDIS

Navigation: Documentation / Collective variables / CV:MDIS

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Distance

DD, DIS, MDIS, MDISG, ODIS, OPOS, OPOS2, ORAD, ORAD2, POS, RAD

Angle

ANG, ANG2, AXANG, AXANG2, DIH, DIH2, PANG, PVANG

Coordination

CNFF, CNGFF, CNSW, CNGSW, CNRF, CNGRF

Shape

ACYL, ASPH, EVEC, PMGTD, PMOGT, PLANE, RGYR, RMSDT, SANIS

Nucleic Acids

NALBPP, NASBPP, NASBPPOLD, NALSTP, NASSTP, NASSTPOLD, NASBO, NAPBO, NABEND

Puckering

PUCK6Q, PUCK6P, PUCK6T, PUCK5Q, PUCK5P

Special

WORMPOS, WORMANG

Energy

POT, EGAP

Algebra

ADD, SUB, MULT, DIV, FSWITCH, RSWITCH

Definition

The minimum value of atom pair distances. To ensure that the collective variable is a continuous function a probabilistic definition is used. This is an approximation providing good estimate of minimal distance. In most cases it provides a value slighter higher than a real minimum distance. However for degenerate situations, where more than one atom pair distance is very close to a minimum value, the value of collective variable will be lower than this minimum value.

$\xi = - \beta * ln \left( \sum_{i=1}^{pairs} e^{ - \frac{d_i}{\beta} }\right)$

Non-degenerate case:

$\xi \geq d_{minimum}$

Degenerate case (n_g is degree of degeneracy):

$\xi \doteq d_{minimum} - \beta*ln(n_g)$

PBC note: The minimum-image convention is apllied to all atom pair distances if the fenable_pbc option is activated.

Specification

Section name: MDIS

Key	Type	Default	Description
name	string		unique CV name
beta	real	1.0	factor β
pair	mask mask		two masks specifying the atom pair. Each mask can hold only one atom. This line is repeating until all atom pairs are specified.

Keys in bold are mandatory.