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

Eudes Fileti fileti at ufabc.edu.br
Thu Aug 16 12:38:14 CEST 2007

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
totalizing 300ps, in ensemble NVT. (Could you suggest something more

I believe that if I start from a configuration with molecules randomly
distributed I would get better
results than a ordinated configuration.

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.
And about this, would you a topology or a equilibrated box for the toluene?

Thanks again.

Message: 4
Date: Thu, 16 Aug 2007 08:35:26 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Potential energy positive. Can be?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <46C37FAE.8070206 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Eudes Fileti wrote:
> Hi gmx users,
> I have tried to simulate a box with 1000 molecules of toluene
> and I always have obtained a positive value for the potential energy.
> I have used three different models of potential (with and without 14
> interactions)
> and all of them provides a positive value for energy. I must be falling in
> some error or making some wrong analysis but I do not know what.
> Below I put the average values that I got from the simulations that I
> If somebody will be able to help me, I will be grateful!

How are you equilibrating these structures? For how long are you doing so?

> Two questions about these results:
> # Why are so larger the values for LJ-14?

Because they're from atoms near each other. You don't just turn them on
and off to suit the phase of the moon, you need to choose whether
they're included according to how the force field was developed and is
intended to be used. Search GROMACS manual for OPLS to see what is
recommended, and/or read the original OPLS paper (reference in the
GROMACS manual).

> # How can I compose the potential energy from the components?
> Would not be U = LJ + Coul + bond + ang + dihed ? And LJ-14?

You add them up. Every energy term that isn't kinetic or total is a
potential energy.


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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