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 <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re: Potential energy positive. Can be? To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> 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 -- _______________________________________ 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 http://cromo.ufabc.edu.br/~fileti/
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