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?)
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. eef Message: 4 Date: Thu, 16 Aug 2007 08:35:26 +1000 From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Potential energy positive. Can be? To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> 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 made. > 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. 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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