[gmx-users] mass-weighting and normal mode analysis

Lei Zhou zhoumadison at gmail.com
Thu Nov 2 17:49:22 CET 2006

Dear GMX-users,

I am trying to setup the normal mode analysis, using mdrun to generate
hessian matrix and g_nmeig to do the analysis. However, I am confused about
the mass-weighting treatment related to these two programs.
question 1:  is the hessian matrix output from mdrun (nm.mtx) mass-weighted
or not?
question 2: My understanding is that the nm.mtx from mdrun is not
mass-weighted. Thus, I have to use the default setting of g_nmeig  (-m yes)
to devide the hessian matrix by the product of sqrt(m1*m2) (see line 145 in
gmx_nmeig.c of 3.3.1). With this setting (-m yes), g_nmeig will mass-scale
the eigenvector output to plain cartesian form (see line 162 in gmx_nmeig.c
of 3.3.1), but the eigenvectors are not orthogonal anymore. If I still want
the hessien matrix to be mass-weighted but without mass-scaling to the
eigenvector output, I have manually turn off the second "bM" flag in
gmx_nmeig.c (line 162 in gmx_nmeig.x)?

Thank you in advance.

Lei Zhou
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