I am attempting to pull a ligand through a channel protein. I have setup the umbrella sampling code and it seems to be working just fine except I get large jumps in the deviation of each pulled group from its restrained position at 1 ps intervals. I am pulling three groups all relative to the backbone(reference group) of the protein only in the Z dimension. My output is as follows. I am running 3.3.1 (I have to use 3.3.1 as I am using a windows cluster for my simulations). Any ideas?
0.994000 -0.033192 0.996000 -0.033191 0.998000 -0.033189 1.000000 -0.099242 1.002000 -0.099240 1.004000 -0.099237 1.992000 -0.099218 1.994000 -0.099220 1.996000 -0.099222 1.998000 -0.099223 2.000000 -0.100077 2.002000 -0.100077 2.004000 -0.100077 2.006000 -0.100076 8.994000 -0.107520 8.996000 -0.107503 8.998000 -0.107486 9.000000 -0.105328 9.002001 -0.105314 9.004001 -0.105302 9.006001 -0.105293 -- Ilya Chorny Ph.D.
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