[gmx-users] Spacing between adjacent umbrella sampling windows

[Justin Lemkul]

On 2/3/14, 6:44 AM, Arunima Shilpi wrote:
> Hello sir
>
> In Umbrella sampling I have considered 0.15nm spacing between sampling
> windows. I have query as to whether the frames selected should in the
> increasing order or the selection of the frames can be random. Here I am
> providing the details of the frames
> selected.
>
> S.No Frames   dist   d_dist(nm)
>
> 0.     269          4.33    0
> 1.     118          4.48    0.15
> 2.     132          4.69    0.19
> 3.     489          4.84    0.15
> 4.     152          5.00    0.16
> 5.     167          5.15    0.15
> 6.     174          5.30    0.15
> 7.     183          5.45    0.15
> 8.     380          5.63    0.18
> 9.     411          5.75    0.12
> 10.   422          5.93    0.18
> 11.   446          6.06    0.16
> 12.   375          6.22    0.16
> 13.   252          6.37    0.15
> 14.   274          6.52    0.15
> 15.   453          6.67    0.15
> 16.   458          6.83    0.16
>
>   Here you can see the first frame is selected from 269 while the next frame
> is 118
>
> I request you to kindly guide me as to whetehr frame selection is correctly
> done.
>

I doubt the order of the frames is relevant, as you can generate configurations 
in a number of ways.  Some lead to steady increases along the reaction 
coordinate, others don't.  You haven't told us how you generated the 
configurations.  The main point is to get suitable starting structures that are 
appropriately spaced along the reaction coordinate.  It appears you have done that.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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