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

Marc Baaden baaden at smplinux.de
Tue Jan 23 10:28:16 CET 2007


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??


>>> Mark Abraham said:
 >> [..] The way to get a subset of the bonded 
 >> interactions is to only define in the .top file that set in which you 
 >> are interested. You don't mess with the atom definitions however. For 
 >> speed, turn off evaluation of all the non-bonded interactions somehow.

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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