[gmx-users] Re: Potential energy positive. Can be?

Janne Hirvi janne.hirvi at joensuu.fi
Thu Aug 16 18:46:20 CEST 2007


I am just wondering that why the potential energy couldnt be positive? It must
have been negative after minimization at 0 K, but in the simulation at specific
temperature the energy of the intramolecular interactions increases increasing
the potential energy...


> Dear Mark,
> Thank you for the link. It was useful.
> I have choosen the volume using the editiconf by setting
> the experimental density for toluene. In fact, my potential
> can be wrong.
> So, I asked you if you would have a topology or an equilibrated box for the
> toluene, since this could be very useful to me.
> (but my text was not understandable, sorry).
> Thanks so much.
> eef
> Message: 5
> Date: Fri, 17 Aug 2007 01:16:36 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: Potential energy positive. Can be?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <46C46A54.5000408 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Eudes Fileti wrote:
> > Dear Mark, thank you for your reply.
> >
> > For equilibration of the system, firstly I generated a ordinated lattice
> > of 10x10x10 molecules.
> > After, I carried out successive minimization runs (with STEEP and
> > L-BFGS) up to the system
> > to reach the convergence for these methods and in the sequence I
> > performed simulations
> > totalizing 300ps, in ensemble NVT. (Could you suggest something more
> > appropriate?)
> Check out
> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation, in
> particular, how did you choose your volume? (and thus density and
> pressure?) Is this reasonable?
> > I believe that if I start from a configuration with molecules randomly
> > distributed I would get better
> > results than a ordinated configuration.
> As soon as you're generating random velocities, it won't matter at all
> whether the starting configuration was ordered or not. After 10ps or
> less you won't be able to see any ordering.
> > I have created the potential for the toluene from of the potential of
> > the benzene and
> > and it seemed the sufficiently reasonable, compared to others potentials
> > from literature.
> "Looking reasonable" is not a sufficient criterion if you want to
> publish these results. You're simulating a complex balance of different
> interactions and our intuition is poorly-trained to see what is good or
> not in this context. The only measure of quality is the ability to
> reproduce (experimental) observables. Hence my point about using an
> existing forcefield in exactly the same way, and not making something
> up.
> The fact that you are getting positive energies suggests that at least
> on of the above issues is a significant problem for your system.
>  > And about this, would you a topology or a equilibrated box for the
> toluene?
> I don't understand you.
> Mark

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