Alif M Latif wrote:
Dear GROMACS users,
Thanks for all the replies. They're very helpful. Actually, i have
no expertise in this field around me. Moreover i'm from chemistry, so
statistical and quantum mechanics are no familiar to me. Thats made my
progress become slower (but not impossible right?).
No, not impossible, but reading some textbook material will be
mandatory. It's very easy to do a simulation that doesn't crash that
doesn't have any correlation with the physical world.
I have done several simualtions using the .mdp file that i modify from
the example included in the online manual. I'm using the OPLS-AA force
field with the reason i'm doing liquid simulations. I have succeeded in
doing some simulations (as a practice), got some problems and i solved
it most based on these helpful mailing-lists. Its just that i wan to
make sure what i'm doing is right until now.
Well that depends what you want to measure, and what force field you're
using. The latter are developed for particular sets of parameters and
lose some validity outside that.
I am doing MD simulation on the mixture of Oleyl oleate (palm oil ester)
/ Sorbitan Monolaurate (Surfactant) in water. The composition is based
on experimental results. I packed these molecules using Packmol
(excluding water).I added water molecules using genbox in calculated box
size. After conjugated-gradients and steepest descents energy
minimizations, i run MD simulation.
There's nothing obviously wrong with your .mdp file, but you need to run
an equilibration regime. Read the literature looking for similar
simulations and see what they do, and check out
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
Mark
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