[gmx-users] g_rmsdist

[Anton Feenstra]

Marc Bruning wrote:

> Dear list,
> 
> the *.gro input of an MD run and the 0th frame from the resulting trajectory 
> show no structural difference, if I export them as pdbs and compare them 
> visually or via RMSD. But if I compare input and 0th frame as *gro files to 
> one and the same *tpr file using g_rmsdist they show a difference in RMSD 
> values of nearly 0.5 nm. Does anyone have an idea why this happens?

Shouldn't happen obviously, but your explanation is a bit hazy to me.
So you did something like:
'editconf -f topol.tpr -o topol.pdb' and 'trjconv -dump 0 dump.pdb'
   and got basically identical structures, but what did you do in the
other case? You compared conf.gro (input to grompp) and 'dump.gro' to
'topol.tpr' and got differences?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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