Hi! I am just wondering that why the potential energy couldnt be positive? It must have been negative after minimization at 0 K, but in the simulation at specific temperature the energy of the intramolecular interactions increases increasing the potential energy...
Janne > 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 <[email protected]> > 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 > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
