[gmx-users] Umbrella Pulling

[Steven Neumann]

Thank you Justin!

On Mon, Feb 13, 2012 at 2:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Steven Neumann wrote:
>
>> Thank you Justin. I run my pulling using two force constant for pulling.
>> K1=100 and K1=200
>> Please, see attached plots of force vs time. Is there any criteria to
>> adjust pulling constant? Would you suggest running it for a longer time?
>>
>
> I know of no systematic study for choosing a force constant.  Guessing
> wildly at what's going on, I'd say you need longer simulations as it
> appears you have only just caused dissociation towards the end of the 500
> ps.
>
> -Justin
>
> Steven
>>
>> On Mon, Feb 13, 2012 at 1:11 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Steven Neumann wrote:
>>
>>        Dear Gmx Users,
>>         Is it always required to restrained positions of the protein
>>        while pulling your ligand? My system is made of 10 ligands
>>        attached to my protein surface. I am pulling one of them.
>>
>>
>>    No, it is not required.  I assume you've gotten this idea from my
>>    tutorial - the restraints there were used for a very specific
>>    purpose (detailed in the paper linked from the tutorial).
>>
>>
>>        I have just seen trajectory of pulling my ligand without
>>        restraining positions of protein and 9 remaining ligands. My
>>        ligand while pulling also pulled the protein with itself (for 1
>>        nm distance) and then splited. Is is this approach more reliable?
>>
>>
>>    If your goal is umbrella sampling, you need only generate a series
>>    of reasonable starting configurations along a defined reaction
>>    coordinate.  The absolute positions are irrelevant; it is the
>>    relative distance that matters.
>>
>>    -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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>>
> --
> ==============================**==========
>
> 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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