[gmx-users] using g_energy

[sang eun jee]

Dear Mark Abraham

I changed contraint variables and can generate bond energy terms.
Thanks for you help!!!

Sangeun Jee

On Fri, Mar 6, 2015 at 6:18 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

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