Hi All,
I had ran this polymer system in NAMD using a psf and generated dcd
files. I am trying to use these files for generating the eigen values
and vectors using the matrix command in ptraj and mass weighted covariance
option.
./ptraj10 pnip_ww_30_charmm.psf
trajin pnipww_30_275.dcd
matrix mwcovar name mwcovar byatom
analyze matrix mwcovar out evecs.dat thermo vecs 5
go
Ptraj reads the psf and trajectory and finally does not do the analyze
matrix
Warning in analyzeMatrix: dsaupd returned info = 3
IPARAM(5) = 0
I also get a bunch of NAN in the mwcovar.dat matrix. However covariance
matrix, distance matrix and correl
are generated correctly.
Can anyone please help.
thanks,
ganesh
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Received on Mon Sep 17 2012 - 13:00:02 PDT
