[gmx-users] regarding :RMSIP calculation

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 18 21:54:42 CEST 2008

Hi Sanjay,

You searched maybe..., but not good enough.
Anyway, suits me for knowing that it sometimes helps adding my name to
the search query :p :p :p


Hope it helps,


On Thu, Sep 18, 2008 at 1:29 PM,  <sanjay23 at iitb.ac.in> wrote:
> dear groacs users
> I want to calculate r.m.s.i.p for exploring convergence of my system and
> motions of two different proteins,i divided my trajectory in two equal
> parts and did  g_covar for getting eigenvectors and corresponding
> eigenvector trjectory as trr file for C-alpha atom of 10 eigenvectors.even
> i know how to calculate RMSIP by trr file in Matlab but it is more time
> taking process because my system is quite large (509 residues).I need a
> script or tools to calculate it. before writting this mail i searched in
> gmx- mailing list and i did not find any script for same.
> need your help!
> thanks in advance.
> sanjay upadhyay
> research scholar
> proein dynamics lab
> IIT bombay India
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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