And if u understand you can reduce the restraints in one simulation
run....however first u should understand how this works....
On Jul 24, 2016 11:48 PM, wrote:
Can u pls read the following:
Finally, we vary the weight of the restraints using type='REST'. This
affects the force constants (rk2 and rk3) we had input in the restraint
file, and the effective force constant is multiplied by the weight we give
the restraints. We will gradually increase the weight from 0.1 to 1 between
step 0 and step 3000. Starting with a smaller weight on the restraints
ensures that large violations in the initial structure do not cause the
system to blow up, and that the structure will quickly adjust in the
beginnning of the simulation to get rid of the really high violations. For
the rest of the run (step 3001 to 20000), we will keep the weight of the
restraints at 1. Following that, we end the weight change section with
type='END'.
I took this from the following link:
www.uni-koeln.de/themen/chemie/software/amber7/tutorial/dna_NMR/nmr_dna_tutorial.htm
It will make u understand the things...
I hope this helps....
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Received on Mon Jul 25 2016 - 01:00:03 PDT
