[gmx-users] Re: Umbrella Sampling

[Ilya Chorny]

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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080130/65737afe/attachment.html>