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
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