[gmx-users] factors effecting the simulation

bhargavi ch bhargavi035 at gmail.com
Wed Mar 25 14:28:43 CET 2009


We were working on the simulation of protein which has 3 chains (trimer) and
each chain with a length of 80 amino acids. We have done the simulation for
5ns.We have observed a sudden shoot up in the RMS at 4ns so we continued
simulating it to 10ns .The peak which started at 4ns extended till 8ns
because of molecule breakage into monomer and dimer. we have also mutated
some surface hydrophobic amino acid  and dint observe shoot up in any of the
mutated simulations. We have also observed the same shoot in the case of X
ray crystallographic structure of template protein, when we did it for 10 ps
simulation. We have done position Restraint Dynamics for 100 ps. What are
the parameters i need to adjust during the simulation to get a stabilized
modeled structure?? Does the PR parameters have any effect on simulation??


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