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

bhargavi ch bhargavi035 at gmail.com
Wed Mar 25 12:32:06 CET 2009


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.


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