[gmx-users] (no subject)

bhargavi ch bhargavi035 at gmail.com
Wed Mar 25 13:16:00 CET 2009


I am working on 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 shoot up in the RMS 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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