[gmx-users] re: Self-assembly simulation of lipids

[Mark Abraham]

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