Perform isotropic reoreientational eigenmode dynamics analysis using given IRED vectors.
ired [relax freq <MHz> [NHdist <distnh>]] [order <order>] tstep <tstep> tcorr <tcorr> out <filename> [norm] [drct] modes <modesname> [name <output sets name>] [ds2matrix <file>]
[relax freq <MHz> [NHdist <distnh>]] Should only be used when ired vectors represent N-H bonds; calculate correlation times tm for each eigenmode and relaxation rates and NOEs for each N-H vector. ’freq <MHz>’ (required) is the Lamor frequency of the measurement. ’NHdist <distnh>’ specifies the length of the NH bond in Angstroms (default is 1.02).
order <order> Order of the Legendre polynomials to use when calculating spherical harmonics (default 2).
tstep <tstep> Time between snapshots in ps (default 1.0).
tcorr <tcorr> Maximum time to calculate correlation functions for in ps (default 10000.0).
out <filename> Name of file to write output to.
[norm] Normalize all correlation functions, i.e., Cl(t = 0) = Pl(t = 0) = 1:0.
[drct] Use the direct method to calculate correlations instead of FFT; this will be much slower.
modes <modesname> Name of previously calculated eigenmodes corresponding to IRED vectors.
[name <name>] Output data set name.
ds2matrix <file>] If specified, write full delta*S^2 matrix (# IRED vector rows by # eigenmodes columns) to <file>.
<name>[S2] S2 order parameters for each vector.
<name>[Plateau] Plateau values for each vector.
<name>[TauM] TauM values for each vector.
<name>[dS2] Full delta*S^2 matrix.
<name>[T1] T1 relaxation values for each vector.
<name>[T2] T2 relaxation values for each vector.
<name>[NOE] NOEs for each vector.
<name>[Cm(t)]:X Cm(t) function for vector X.
<name>[Cj(t)]:X Cj(t) function for vector X.
Peform IRED[reference] analysis on previously defined IRED vectors (see vector ired) using eigenmodes calculated from those vectors with a previous ’diagmatrix’ command. The number of defined IRED vectors should match the number of eigenmodes calculated. Autocorrelation functions for each mode and the corresponding correlation time tm will be written to filename.cmt. Autocorrelation functions for each vector will be written to filename.cjt.
Relaxation rates and NOEs for each N-H vector will be written to <filename> or added to the the end of the standard output. For the calculation of tm the normalized correlation functions and only the first third of the analyzed time steps will be used. For further information on the convergence of correlation functions see reference.
Example of IRED in Cpptraj
In cpptraj, IRED analysis can now be performed in one pass (as opposed to the two passes previously required in ptraj). First, IRED vectors are defined (in this case for N-H bonds) and an IRED matrix is calculated and analyzed. The IRED vectors are then projected onto the calculated IRED eigenvectors in the ired analysis command to calculate the time correlation functions. If the parameter order is specified, order parameters based
on IRED are calculated. By specifying the relax parameter, relaxation rates and NOEs can be obtained for each N-H vector. Note that the order of the IRED matrix should be the same as the one specified for IRED analysis.
# Define N-H IRED vectors vector v0 @5 ired @6 vector v1 @7 ired @8 ... vector v5 @15 ired @16 vector v6 @17 ired @18‘ # Define IRED matrix using all previous IRED vectors matrix ired name matired order 2 # Diagonalize IRED matrix diagmatrix matired vecs 6 out ired.vec name ired.vec # Perform IRED analysis ired relax NHdist 1.02 freq 500.0 tstep 1.0 tcorr 100.0 out v0.out noefile noe order 2