[gmx-users] what factors effetc the simulation during energy minimization

[Mark Abraham]

bhargavi ch wrote:
> hi..
>  
> I have been doing the simulation of protein which has 3 chains 
> (trimer)and each chain with a length of 80 amino acids. I have done the 
> simulation for 5ns. I have observed a sudden peak at 4ns  so i continued 
> simulating it to 10ns ..the peak which started at 4ns extended till 8ns 
> .i have extracted the pdbs at this particular time frames.i found that 
> the trimer is been spilt into monomer and dimer.i wanted to know exactly 
> what are the parameters i need to adjust during the simulation to get a 
> stabilised modelled structure.

Energy minimization does not occur over time, so you are mis-describing 
something here.

You haven't told us what you're observing to peak at 4ns.

Perhaps you need to understand some material here 
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions

Mark