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

Eudes Fileti fileti at ufabc.edu.br
Thu Aug 16 18:10:37 CEST 2007

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.

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

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

I don't understand you.


Eudes Eterno Fileti
Centro de Ciência Naturais e Humanas
Universidade Federal do ABC
Rua Catequese, 242 - 3º Andar
09090-400  Santo André - SP Brasil
Tel: +55 11 4437-1600 ramal 408
skype: eefileti
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