AW: [gmx-users] Bond force constant for GROMOS

Rausch, Felix frausch at ipb-halle.de
Wed Jul 6 10:23:54 CEST 2011

```Hey Javier,

Thank you very much!

I already read the manual, but somehow didn't get the point. Now its clear, thanks.

Felix

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Von: gmx-users-bounces at gromacs.org im Auftrag von Javier Cerezo
Gesendet: Mi 06.07.2011 09:40
An: gmx-users at gromacs.org
Betreff: Re: [gmx-users] Bond force constant for GROMOS

Hi Felix

Take a look to 4.2.1 section in the manual. Gromos force constants (k^b) has this extra nm-2 factor because they are defined as:
2 k^b bij^2 = k^{b,harm}  (equation 4.39 in the manual version 4.5.4)

So you have to divide your derived harmonic force constants (in KJ/(mol*nm^2) by 2 and bij^2 (equilibrium distance or ideal bond length as stated in gromos files) to get the gromos one (k^b). It could also be useful for you to visit the new GROMOS website as there is some free downloadable FF documentation.

Javier

El 06/07/11 08:48, Rausch, Felix escribió:

Dear Gromacs-users,

I would like to add a new bond type to the ffbonded.itp of the Gromos53a6 force field. For that, I tried to obtain the force constant for my new bond by performing vibrational frequency calculations with Gaussian. With that, I obtained the force constant in mDyne/A.
My problem is now: How can I convert this value to kJ/(mol*nm(4)) as required for the force field? I already tried, but I only end up at kJ/(mol*nm(2)). Also arround the web I could only find a factor for conversion of mDyne/A to kJ/(mol*nm(2)). Is there any trick or hint you can give me about that?

Felix

--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry