[gmx-users] (no subject)

[Justin A. Lemkul]

Sai Janani Ganesan wrote:
> Hi,
> 
> 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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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