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.
Erik
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
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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