[gmx-users] Entropy calculation from normal modes

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Mon Oct 11 17:14:38 CEST 2004


It sounds as if you are trying to recreate the MM_PBSA approach from
Amber. That package has a nice perl script which does all of these
things (PB calculations, normal more analysis) automatically. The
approach I'm using at the moment is to run my trajectories in
Gromacs, convert them to Amber format and analyse with Amber. Of
course this requires using a ff which runs in Amber, (and paying for
a license for the non-GPL Amber package), which may cause you more
problems than you solve. 


---- Message from Marc Baaden <baaden at smplinux.de> at 2004-10-11
11:29:08 ------
>I would like to calculate entropy estimates from normal modes
>obtained with Gromacs, and wonder whether anybody has experience
>with this approach, and in an ideal world might be willing to
>share eventual post-processing scripts for the treatment of the
>raw normal mode data.
>Entropy estimation from covariance analysis seems to be an easier
>route, but heavily dependent on convergence issues, which is why
>I am not keen on using this approach.
>Any other suggestions ?
>  Marc
> Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
> FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217
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