[gmx-users] (no subject)

[Sai Janani Ganesan]

Oh, thanks!

On Thu, Oct 6, 2011 at 7:59 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Sai Janani Ganesan wrote:
>
>> 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?
>>
>>
> When setting "distance" as the pull_geometry, only pull_dim is used;
> pull_vec is ignored.  If you want to define vectors, use the "direction"
> pull_geometry.
>
> -Justin
>
>  Thanks,
>> Sai
>>
>>
>>
>>
>> On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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 <http://vt.edu> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
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>> --
>>
>> /"Every sentence I utter must be understood not as an affirmation but as a
>> question." - Niels Bohr/
>>
>
> --
> ==============================**==========
>
> 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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*"Every sentence I utter must be understood not as an affirmation but as a
question." - Niels Bohr*
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