[gmx-users] how to calculate internal energy for energygroups?

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 23 14:21:35 CET 2007

Marc Baaden wrote:
> Hi,
> thanks for the hint, but doing this to calculate the internal energy for
> each residue in a 300-residue protein seems to require quite some serious
> scripting and topology file parsing, in particular as the residue number
> is not referred to in the bonded, angle etc. parts of the topology..
> ..unless such a script already exists in the directory of some kind
> Gromacs user who would be willing to contribute it to the community??
Maybe we should go back one step. The reason this is not implemented is 
because we thought it would be unnecessary. In addition, if you would do 
it per residue how would you categorize e.g. the dihedral terms with one 
atom in one residue and three atoms in another? Of course you can define 
something, but what does it mean?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list