[gmx-users] (no subject)

[Sai Janani Ganesan]

Hi,

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
anything?

Thanks,
Sai



On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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