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