[gmx-users] Normal mode analysis

Erik Lindahl lindahl at sbc.su.se
Fri Dec 9 20:25:49 CET 2005


> the emtol ant emstep parameters. But after each step (mdrun  
> execution) I
> didn't use the .trr file for the new grompp execution. Maybe the  
> error is in
> this point.
> Anyway I will redo everything and I'll double check these things

That's the problem. "Machine precision" means we were moving  
coordinates in the order of 1e-15, but the output .gro file truncates  
all values to three decimals (=horribly bad energies).

You _need_ to use the -t option to read the full precision input  
coordinates from the binary minimization trajectory.



Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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