Dear Mark, thank you for your reply.<br><br>For equilibration of the system, firstly I generated a ordinated lattice of 10x10x10 molecules. <br>After, I carried out successive minimization runs (with STEEP and
L-BFGS) up to the system <br>to reach the convergence for these methods
and in the sequence I performed simulations <br>totalizing
300ps, in ensemble NVT. (Could you suggest something more appropriate?) <br><br>I
believe that if I start from a configuration with molecules randomly distributed I would get better <br>results than a ordinated configuration. <br><br>I have created the potential for the toluene from of the potential of the benzene and
<br>and it seemed the
sufficiently reasonable, compared to others potentials from literature. <br>And about this, would you a topology or a equilibrated box for
the toluene?<br><br>Thanks again.<br>eef<br><br>Message: 4<br>Date: Thu, 16 Aug 2007 08:35:26 +1000<br>From: Mark Abraham <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:Mark.Abraham@anu.edu.au">
Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] Potential energy positive. Can be?<br>To: Discussion list for GROMACS users <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a>><br>Message-ID: <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:46C37FAE.8070206@anu.edu.au">46C37FAE.8070206@anu.edu.au</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
<br><br>Eudes Fileti wrote:<br>> Hi gmx users,<br>> I have tried to simulate a box with 1000 molecules of toluene<br>> and I always have obtained a positive value for the potential energy.<br>> I have used three different models of potential (with and without 14
<br>> interactions)<br>> and all of them provides a positive value for energy. I must be falling in<br>> some error or making some wrong analysis but I do not know what.<br>> Below I put the average values that I got from the simulations that I made.
<br>> If somebody will be able to help me, I will be grateful!<br><br>How are you equilibrating these structures? For how long are you doing so?<br><br>> Two questions about these results:<br>> # Why are so larger the values for LJ-14?
<br><br>Because they're from atoms near each other. You don't just turn them on<br>and off to suit the phase of the moon, you need to choose whether<br>they're included according to how the force field was developed and is
<br>intended to be used. Search GROMACS manual for OPLS to see what is<br>recommended, and/or read the original OPLS paper (reference in the<br>GROMACS manual).<br><br>> # How can I compose the potential energy from the components?
<br>> Would not be U = LJ + Coul + bond + ang + dihed ? And LJ-14?<br><br>You add them up. Every energy term that isn't kinetic or total is a<br>potential energy.<br><br>Mark<br><br><br>_______________________________________
<br>Eudes Eterno Fileti<br>Centro de Ciência Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Catequese, 242 - 3º Andar<br>09090-400 Santo André - SP Brasil<br>Tel: +55 11 4437-1600 ramal 408<br>skype: eefileti<br>
<a href="http://cromo.ufabc.edu.br/~fileti/">http://cromo.ufabc.edu.br/~fileti/</a>