[gmx-users] (no subject)
Sai Janani Ganesan
sai.gans at gmail.com
Fri Oct 7 01:58:17 CEST 2011
Thanks for the reply!
I tried the rates, and only the terminal with positive rate gets pulled.
The first and the last amino acids are spatially oriented one behind the
other. I think defining a vector might work better, but I am not sure why
nothing happens when I define a pull_vec1 and pull_vec2. Am I missing
On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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