YARM - Yet Another Relaxation Matrix program

YARM: Yet Another Relaxation Matrix program
A program for performing nuclear spin relaxation calculations

These are the subroutines that perform NMR relaxation calculations.

&calcSpecDens

Summary:
Calculates the rigid body spectral densities of the molecule described by the associative array %YarmModel.

Usage:
&writeSpecDens( \%YarmModel );
or
&writeSpecDens( \%YarmModel, "ascii" );

Description:
If you want to see a humanly readable version of the binary output file, specify "ascii" as the second input parameter, as shown above. This will generate a file named "spec_dens_mt.asc" in the yarm_working subrdirectory that can be examined with a text editor. Additionally, a number of test calculations will be performed that can be examined to insure the calculations are working correctly.

Example:

&calcR1

Summary:
Calculates the R1 relaxation rates of the nuclei contained in the %YarmModel.

Usage:
%R1 = &calcR1( \%YarmModel );
or
%R1 = &calcR1( \%YarmModel, "time" );

Description:
This routine calculates the R1 relaxation rates for all nuclei contained in $YarmModel{xyz_nmr} (the NMR active nuclei). The spectral densities must be contained in a file called "yarm_working/spec_dens_mt.bin", created previously using the calcSpecDens subroutine.

If "time" is specified, then the relaxation values are returned as times rather than rates.

Example:

&calcR2

Summary:
Calculates the R2 relaxation rates

Usage:
%R2 = &calcR2( \%YarmModel );
or
%R2 = &calcR2( \%YarmModel, "time" );

Description:
This routine calculates the R2 relaxation rates for all nmr active nuclei contained in $YarmModel{xyz_nmr}. The spectral densities must have been created previously using the calcSpecDens subroutine.

If "time" is specified, then the relaxation values are returned as times rather than rates.

Example:

&calcSSNOE

Summary:
Calculates the steady state NOE enhancement

Usage:
%ssNOE = &calcSSNOE( \%YarmMode );
or
%ssNOE = &calcSSNOE( \%YarmModel, "time" );

Description:
This routine calculates the ssNOE relaxation rates for all nmr active nuclei contained in $YarmModel{xyz_nmr}. The spectral densities must have been created previously using the calcSpecDens subroutine.

If "time" is specified, then the relaxation values are returned as times rather than rates.

Example:

&calcR1_R2_SSNOE

Summary:
Calculates all three relaxation rates, R1, R2, ssNOE simultaneously Usage:
($refR1, $refR2, $refNOE ) = &calcR1_R2_SSNOE( \%YarmMode );
or
($refR1, $refR2, $refNOE ) = &calcR1_R2_SSNOE( \%YarmModel, "time" );

Description:

If "time" is specified, then the relaxation values are returned as times rather than rates.

Example:

&calcMin_Dyn

Summary:
Calculates the intramolecular dynamics variables

Usage:
( $ref_Sf2, $ref_ti, $ref_X2 ) =
&calcMin_Dyn( \%YarmModel, \%R1exp, \%R2exp, \%ssNOEexp, $exp_type, $nruns );

%Sf2 = %$ref_Sf2;
%ti = %$ref_ti;
%X2 = %$ref_X2;

Description:
This routine calculates the best intramolecular dynamics for the molecule specified by %YarmModel by using comparing simulated and experimentally measured R1, R2 and ssNOE rates. Returned are the Sf2, ti and X2 values for each nucleus, and their associate error.

$nruns determines how many Monte Carlo simulations to perform in the error analysis. If set to 1, no Monte Carlo is performed, and the error is returned as "-1".

Example:

&calcMin_Rot_Dyn

Summary:

Usage:
( $txx, $tyy, $tzz, $x2, $txx_err, $tyy_err, $tzz_err, $x2_err ) =
&calcMin_Rot_Dyn( \%YarmModel, \%R1exp, \%R2exp, $nfit, $nruns );

Description:
This routine calculates the best correlation time for the molecule specified by %YarmModel by using comparing the simulated R2/R1 relaxation times to those measured experimentally. %R1exp and %R2exp are 1D hashes containing the experimetnal R1 and R2 rates, and their associated errors. $nruns is the number of Monte Carlo runs to perform to generate the error values. If $nruns is set to 1, the Monte Carlo is not performed, and the error is returned as "-1".

Example: