[gmx-users] gromacs harmonic bond constant

Erik Marklund erikm at xray.bmc.uu.se
Fri Feb 5 16:39:15 CET 2010

It depends on the function type. See the table "Intramolecular 
interaction definitions" in chapter 5 of the gromacs manual. There you 
can se the units associated with the different kinds of interactions.


Vitaly V. Chaban skrev:
> Hi,
> In what units does gromacs MD engine treats harmonic bond constants?
> In the tutorial, there is a hint about fourth-power potential (related
> to GROMOS-96 FF) which I guess should have a constant in
> [kJ/mol/nm^4], but not in [kJ/mol/nm^2]. Although it seems by the
> absolute value that in the existing FFs (.../top/) including GROMOS96
> they appear in [kJ/mol/nm^2].
> If the own FF is used, in what units should one type the values of k_b
> in topology file for GROMPP to understand it correctly? My variant is
> [kJ/mol/nm^2]. Please let me know if I'm true.
> Thanks.

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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