[gmx-users] (no subject)
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 6 15:14:46 CEST 2011
Sai Janani Ganesan wrote:
> 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
I suspect the % signs will mess things up, but probably will give a fatal error,
if nothing else.
> pull_rate1 = 0.002
> pull_k1 = 1000
> pull_rate2 = 0.002
> pull_k2 = 1000
Here's the problem. You're telling the two pulled groups to move in the same
direction. With "distance" geometry, the selections are a bit more simplistic.
If you set pull_rate1 to -0.002 and pull_rate2 to 0.002, the groups will be
pulled in opposite directions. Otherwise, you're just towing your protein along
in the box.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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