[gmx-users] Pull code vs. manual pull for umbrella sampling

Justin Lemkul jalemkul at vt.edu
Fri Jan 24 21:57:33 CET 2014

On 1/24/14, 3:50 PM, shivangi nangia wrote:
> Dear Justin,
> Okay, so I have multiple configurations of protein and bi-layer system (30
> initial configurations) at varied distances (in steps of 0.05 nm).
> The protein has been moved away with respect to its COM.
> So I have "manually" pulled the protein away from the bi-layer instead of using
> the pull code.
> I have run MD simulations for each of these configurations.
> I need to use g_wham to calculate the PMF and for that I need the pullx.xvg files.

It won't be possible.  What you did wasn't umbrella sampling, it was just MD. 
If there is no restraint potential applied during the simulations in each of the 
sampling windows, there's nothing to de-bias to reconstruct a free energy profile.

You can generate the configurations in any manner you like (manually or by using 
the pull code), but the umbrella sampling itself requires the use of the pull code.



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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