Hi GMX Users, I am doing Justin tutorial of Umbrella sampling. I have just finished continous pulling of chainA from the reference chainB. I have some questions. I looked at the trajectory of pulling and it has began with dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My question is why? As you apply pulling with the constant force to the COM of the whole chain why does it start with terminal residue following then one by one? Why not the middle one or any other?
The second thing I would like to extract starting configurations from from my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense as the ChainA is still within ChainB. I would like to use configurations: 0 - 0.50 50 - 0.52 100 - 0.51 150 - 0.51 200 - 0.62 250 - 2.21 .... 500 - 5.48 My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or this configuration above is ok? Can the spacing in nm vary? And the last thing - is it required to use frames till 189 as the COM varies in this area? Thank you! Steven
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