[gmx-users] (no subject)

Sai Janani Ganesan sai.gans at gmail.com
Thu Oct 6 15:06:51 CEST 2011


I am trying to pull the first from the last amino acid of a protein to
completely unfold the protein in the X direction. I chose the middle amino
acid as the reference, and the groups get pulled in the same direction or
opposite direction (which is what I want) depending on the trial. I am
trying to find a definite method to completely unfold it.

I define a different vector (pull_vec1 and pull_vec2) with +x and -x values
and that does not even pull the protein
I tried using only pull_group1 and pull_group2, without a reference, and
neither groups get pulled.
I chose different references, I do have some success but I don't think it is
the best way to do it.

How do I pull the N and C terminal apart, by simultaneously pulling them in
opposite directions?Why is my vector definition wrong?

This is my pull code:

pull            = umbrella
pull_geometry   = distance

pull_dim        = Y N N
pull_start      = yes
pull_ngroups    = 2
pull_group0     = Chain-C
pull_group1     = Chain-B
pull_group2     = Chain-A

%pull_vec1      = -31 0 0
%pull_vec2      = 31 0 0
pull_rate1      = 0.002
pull_k1         = 1000
pull_rate2      = 0.002
pull_k2         = 1000



*"Every sentence I utter must be understood not as an affirmation but as a
question." - Niels Bohr*
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