| This is part of the colvar module |
Calculates the Paramegnetic Resonance Enhancement intensity ratio between two atoms. The reference atom for the spin label is added with SPINLABEL, the affected atom(s) are give as numbered GROUPA1, GROUPA2, ... The additional parameters needed for the calculation are given as INEPT, the inept time, TAUC the correlation time, OMEGA, the larmor frequency and RTWO for the relaxation time.
- Description of components
The names of the components in this action can be customized by the user in the actions input file. However, in addition to these customizable components the following quantities will always be output
| Quantity | Description |
| pre | the # PRE |
In addition the following quantities can be calculated by employing the keywords listed below
| Quantity | Keyword | Description |
| exp | ADDEXP | the # PRE experimental intensity |
- The atoms involved can be specified using
| SPINLABEL | The atom to be used as the paramagnetic center.. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
| 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... |
- Compulsory keywords
| INEPT | is the INEPT time (in ms). |
| TAUC | is the correlation time (in ns) for this electron-nuclear interaction. |
| OMEGA | is the Larmor frequency of the nuclear spin (in MHz). |
- Options
| NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
| NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |
| ADDEXP | ( default=off ) Set to TRUE if you want to have fixed components with the experimetnal values.
|
| RTWO | The relaxation of the atom/atoms in the corresponding GROUPA of atoms. Keywords like RTWO1, RTWO2, RTWO3,... should be listed. You can use multiple instances of this keyword i.e. RTWO1, RTWO2, RTWO3... |
| PREINT | Add an experimental value for each PRE. You can use multiple instances of this keyword i.e. PREINT1, PREINT2, PREINT3...
|
- Examples
In the following example five PRE intensities are calculated using the distance between the oxigen of the spin label and the backbone hydrogens. Omega is the NMR frequency, RTWO the R2 for the hydrogens, INEPT of 8 ms for the experiment and a TAUC of 1.21 ns
PRE ...
LABEL=HN_pre
INEPT=8
TAUC=1.21
OMEGA=900
SPINLABEL=1818
GROUPA1=86 RTWO1=0.0120272827
GROUPA2=177 RTWO2=0.0263953158
GROUPA3=285 RTWO3=0.0058899829
GROUPA4=335 RTWO4=0.0102072646
GROUPA5=451 RTWO5=0.0086341843
... PRE
PRINT ARG=HN_pre.* FILE=PRE.dat STRIDE=1
1.8.14