[gmx-users] using g_energy

[Mark Abraham]

No, you've used .mdp settings to convert .itp [bonds] into constraints.

Mark

On Sat, Mar 7, 2015 at 12:07 AM, sang eun jee <sangeunjee at gmail.com> wrote:

> Dear Mark Abraham
>
> Thank you very much for your answer.
>  Actually I did not use constraint with *.itp files  when I performed npt
> simulations.I have just used amber99sb ildn forcefield, installed in
> GROMACS package. The fact that "bond energy term" does not appear from
> g_energy means that I don't have bond energy term in my forcefield?
>
> I appreciate your help.
>
> Best Regards,
>
> Sangeun Jee
>
>
>
> On Fri, Mar 6, 2015 at 5:29 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Probably the answer is "don't constrain bond lengths and then expect them
> > to vary" :-)
> >
> > Mark
> > On 06/03/2015 5:21 pm, "sang eun jee" <sangeunjee at gmail.com> wrote:
> >
> > > Dear gromacs users
> > >
> > > Hello.
> > > I am using gromacs  4.6.6 to simulate protein in water solution and
> have
> > > one question about using g_energy.
> > > I am using AMBER99sb-ILDN forcefield, whose forcefield has bonded
> > > terms-bonds, angles, dihedrals and non bonded terms-LJ and coulombic
> > > interactions.
> > >
> > > When using g_energy to analyze the potential, the options included
> > angles,
> > > dihedrals(proper and improper),LJ (sr and 14) and coulombic
> > interactions(sr
> > > and 14) but there is no "bond-bond interaction energy". Could you let
> me
> > > know how I can calculate bond-bond energy term?
> > >
> > > Thanks,
> > >
> > > Sangeun Jee
> > >
> > >
> > > --
> > > Post Doctoral Researcher
> > > School of Materials Science and Engineering
> > > Georgia Institute of Technology
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