[gmx-users] g_rms

Itamar Kass ikass at cc.huji.ac.il
Mon Jan 3 11:36:41 CET 2005

  Happy new year all, I have a question which might sound strange.  While
calculating RMSD (using g_rms) I got strange results.  In order to check it I
calculated the rmsd between two identical structures (I just copy a structure).
 The calculated rmsd was more then a 1.5nm.  The differance between the two
structures was only in the absence of hydrogen in the second structure.
I used:
g_rms -s M2TMP_tet_Kim.pdb -f M2TMP_tet_Kim_2.pdb

Does someone know what is happening here?

Computers are like airconditioners... They don't work well with Windows

| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html

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