[gmx-users] Umbrella Sampling tutorial

[Justin Lemkul]

On 11/9/13 8:22 AM, shahab shariati wrote:
> Daer Justin
>
> I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
>
> The system you considered was the dissociation of a single peptide from the
> growing end of an protofibril.
>
> You considered following parameters:
>
> Chain_B: reference group for pulling.
> Chain_A: group to which pulling force is applied.
> pulling direction was Z.
>
> you placed the center of mass of the protofibril at (3.280, 2.181, 2.4775)
> in a box of dimensions 6.560 x 4.362 x 12 by editconf:
>
> editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560
> 4.362 12.
>
> I have a question:
>
> You said " pull distance must always be less than one-half the length of
> the box vector along which the pulling is being conducted".You pulled a
> total distance of 5.0 nm in a 12.0-nm box, to avoid the complications
> described above.
>
> Why did you used 2.4775? I think 5.0 is true. Please give me more
> explanation. How did you obtained this value?
>

I knew I needed a rectangular box, given the intrinsic geometry of the protein 
complex and the manner in which I was pulling, so I started by building a cubic 
box around the pentamer that satisfied normal minimum image convention criteria 
based on my cutoffs.  I noted its dimensions and extended the box by 5.0 nm 
along z, then added a bit of padding space, because the COM distance itself is 
not the only factor that is important; I had to simultaneously account for the 
fact that I was unfolding a peptide along the reaction coordinate.  So I added a 
bit more space for good measure to avoid spurious PBC interactions at the end of 
the reaction coordinate.  It's all fairly empirical, determined stepwise by 
accounting for the important features of the system.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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