[gmx-users] Umbrella Sampling - Justin tutorial

Steven Neumann s.neumann08 at gmail.com
Wed Nov 16 10:31:32 CET 2011

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!

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111116/2362d418/attachment.html>

More information about the gromacs.org_gmx-users mailing list