[gmx-users] Re: [ gromacs harmonic bond constant
Vitaly V. Chaban
vvchaban at gmail.com
Fri Feb 5 16:45:56 CET 2010
OK. I found my function type "1" and used k_b in [kJ/mol/nm^2].
On Fri, Feb 5, 2010 at 5:39 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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:
>> 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.
> 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
Vitaly V. Chaban, Ph.D.
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