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 gmx-users@gromacs.org
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
