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 <br clear="all">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?<br>
<br>0.994000 -0.033192<br>0.996000 -0.033191<br>0.998000 -0.033189<br>1.000000 -0.099242<br>1.002000 -0.099240<br>1.004000 -0.099237<br><br>1.992000 -0.099218<br>1.994000 -0.099220<br>1.996000 -0.099222<br>
1.998000 -0.099223<br>2.000000 -0.100077<br>2.002000 -0.100077<br>2.004000 -0.100077<br>2.006000 -0.100076<br><br>8.994000 -0.107520<br>8.996000 -0.107503<br>8.998000 -0.107486<br>9.000000 -0.105328<br>
9.002001 -0.105314<br>9.004001 -0.105302<br>9.006001 -0.105293<br><br><br>-- <br>Ilya Chorny Ph.D.<br>