[gmx-users] how to read binary file rmsd.dat

David van der Spoel spoel at xray.bmc.uu.se
Mon Dec 6 09:41:12 CET 2004

On Mon, 2004-12-06 at 11:15 +0530, arnab mukherjee wrote:
> Dear All,
> I am a new user of Gromacs. I was interested in calculation of the
> RMSD values along a trajectory --- for all structures with one
> another. So for a list of N trajectory, I should get a N dimensional
> matrix with N(N-1)/2 independent RMSD values.
> g_rms does this with the option -bin. It generates a xpm impage also. 
>  But I need the values of the matrix in normal ascii format. I tried
> several ways --- includin C and Perl program. But I could not obtain
> the values of  RMSD.

check the source code.

> Can you please tell me how to get the RMSD matrix in nomal ascii
> format or is there another way to get that?
>  Awaiting eagerly for a reply,
> Arnab Mukherjee
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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