[gmx-users] Choose groups for force output

Matteus Lindgren matteus.lindgren at chem.umu.se
Tue Aug 26 14:59:06 CEST 2008

Hi all!


>From an/during an MD simulation of a protein in water or urea solvent I
would like to extract the forces acting on certain protein atoms from the
whole solvent (that is, one protein atom but all solvent) at for example
every 10th timestep.


With nstfout I can set the frequency for output but how can I choose to
output only some of the forces? How to remove the protein intramolecular
forces from the protein – solvent forces? How to choose only some protein

If it is more convenient, perhaps there is a possibility to re-calculate the
forces based on the trajectory file?


Thank you!



Matteus Lindgren 

Graduate student 


Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
Tel: +46 (0)90 786 53 68
e-mail:  <mailto:barbara.addario at chem.umu.se> matteus.lindgren at chem.umu.se


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