NOE

This is part of the colvar module

Calculates the deviation of current distances from experimental NOE derived distances.

NOE distances are calculated between couple of atoms, averaging over equivalent couples, and compared with a set of reference distances. Distances can also be averaged over multiple replicas to perform replica-averaged simulations. Each NOE is defined by two groups containing the same number of atoms and by a reference distance, distances are calculated in pairs.

\[ NOE() = \sum_i^{noes}((\frac{1}{N_{eq}}\sum_j^{N_{eq}} (\frac{1}{r_j^6}))^{\frac{-1}{6}} - d_i^{exp})^2 \]

Reference distances can also be considered as upper limits only, in this case the sum is over a half parabola.

The atoms involved can be specified using

GROUPA	the atoms involved in each of the contacts you wish to calculate. Keywords like GROUPA1, GROUPA2, GROUPA3,... should be listed and one contact will be calculated for each ATOM keyword you specify. You can use multiple instances of this keyword i.e. GROUPA1, GROUPA2, GROUPA3...
GROUPB	the atoms involved in each of the contacts you wish to calculate. Keywords like GROUPB1, GROUPB2, GROUPB3,... should be listed and one contact will be calculated for each ATOM keyword you specify. You can use multiple instances of this keyword i.e. GROUPB1, GROUPB2, GROUPB3...

Compulsory keywords

WRITE_NOE

( default=0 ) Write the back-calculated chemical shifts every # steps.

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
UPPER_LIMITS	( default=off ) Set to TRUE if you want to consider the reference distances as upper limits.
ENSEMBLE	( default=off ) Set to TRUE if you want to average over multiple replicas.
SERIAL	( default=off ) Perform the calculation in serial - for debug purpose

NOEDIST

A compulsory reference distance for a given NOEYou can either specify a global reference value using NOEDIST or one reference value for each contact. You can use multiple instances of this keyword i.e. NOEDIST1, NOEDIST2, NOEDIST3...

Examples

In the following examples three noes are defined, the first is calculated based on the distances of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances 4-15,4-16,8-15,8-16.

NOE ...
GROUPA1=1,3 GROUPB1=2,2 NOEDIST1=0.5
GROUPA2=5 GROUPB2=7 NOEDIST2=0.4
GROUPA3=4,4,8,8 GROUPB3=15,16,15,16 NOEDIST3=0.3
LABEL=noes
... NOE

PRINT ARG=noes FILE=colvar

(See also PRINT)