[gmx-users] Umbrella Pulling

[Justin A. Lemkul]

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://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

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