[gmx-users] what factors effetc the simulation during energy minimization
Mark.Abraham at anu.edu.au
Wed Mar 25 12:40:26 CET 2009
bhargavi ch wrote:
> 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
You haven't told us what you're observing to peak at 4ns.
Perhaps you need to understand some material here
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