[gmx-users] using g_energy

[sang eun jee]

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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-- 
Post Doctoral Researcher
School of Materials Science and Engineering
Georgia Institute of Technology