[gmx-users] Re: [ gromacs harmonic bond constant

[Vitaly V. Chaban]

OK. I found my function type "1" and used k_b in [kJ/mol/nm^2].

Vitaly


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.
>
> 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
> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>
>



-- 
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html