[gmx-users] Principal Components Analysis in Gromacs

James Starlight jmsstarlight at gmail.com
Wed Mar 28 13:31:08 CEST 2012

Dear Gromacs Users!

I have some questions about PCA implemented in Gromacs.

1- I want to increase amplitude of the motions seen on the selected PCs but
I can't found scalling factor option for that.

2- I have calculated MD trajectory for my protein. From this trajectory I
want to find some relevant motions by means of PCA analysis. Also I have
dataset of the experimental structures of that protein where this motion
also presents ( e.g active and innactive conformations of my protein
included in my dataset) As the consequence I want to compare overal
direction of the motion observed along some PCs calculated from MD
trajectory ( it's called EDA) with the motion observed olong other PCs wich
was calculated from the enssemble of the pdb structures. As I've noticed
via  g_anaeig I can compare such datasets by means of -v and -v2 flaggs.
For this purpose I must make trajectory for my X-ray structures at first
and load it with the MD trajectory into the g_anaeig -v md.trr -v2
x_ray.trr. Would this aproach be correct in general ? What should I do if
both of my datasets consist of different number of backbone atoms (due to
some missing residues in the X-ray data) ?

Thanks for help,

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