[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 89

[张正财]

> Date: Fri, 18 Mar 2016 11:43:01 +0100
> From: Josip Lovri? <josip7lovric at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Potential energy of each atom
> Message-ID:
>  <CAHy4cn8TVOt0JeY7yuT2QHwhMsDptabYo2T4qu+vbK1Ze0B0vg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Potential energy for one atom is not well defined physical quantity as far
> as I know, you can only calculate potential energy for at least two body
> (atoms). You need to give more details about what you want and I do not
> know what LAMMPS do.

     Thanks anyway,

     The command "pe/atom" in LAMMPS is described with this : "The per-atom energy is calculated by the various pair, bond, etc potentials defined for the simulation. If no extra keywords are listed, then the potential energy is the sum of pair, bond, angle, dihedral, improper, and kspace energy. If any extra keywords are listed, then only those components are summed to compute the potential energy."

     Maybe it is not easy for GROMACS to output pe/atom.

      Zhengcai
> 
> Josip
> 
> 2016-03-18 11:03 GMT+01:00 ??? <zhangzhengc at mail.iggcas.ac.cn>:
> 
> > > Subject: Re: [gmx-users] Potential energy of each atom
> > > Message-ID: <56EBA4A9.8020905 at xray.bmc.uu.se>
> > > Content-Type: text/plain; charset=UTF-8; format=flowed
> > >
> > > On 18/03/16 03:40, ??? wrote:
> > > > Dear all,
> > > >
> > > >        Could anyone tell me how can I output potential energy of each
> > atom from a trajectory file?
> > > >
> > > What does that mean?
> >
> > Like the command in LAMMPS, "compute pe/atom", I want to display the
> > potential energy of each atom in simulation system. is it possible in
> > gromacs?
> > >
> > > If you have a Na+ and a Cl- in the gas phase Gromacs can compute Coulomb
> > > energy and Lennard Jones energy. But how would you partition that over
> > > atoms?
> > >
> > >
> > >
> > > >        All the best,
> > > >
> > > >       Zhengcai
> > > >
> > > >      Iggcas, CAS
> > > >
> > > >
> > >
> > >
> > > --
> > > David van der Spoel, Ph.D., Professor of Biology
> > > Dept. of Cell & Molec. Biol., Uppsala University.
> > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> > > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> > >
> > >
> >
> >
> >
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> End of gromacs.org_gmx-users Digest, Vol 143, Issue 89
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