feenstra at few.vu.nl
Fri Sep 10 18:18:40 CEST 2004
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?
| | |
| _ _ ___,| 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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