[gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Justin Lemkul jalemkul at vt.edu
Wed Apr 22 14:12:51 CEST 2015

On 4/21/15 6:54 AM, Christopher Neale wrote:
> Dear Mahender:
> It's a real pity that the pull_geometry = position has been removed. So now it's impossible to do umbrella sampling of a solute across a lipid bilayer properly? Anyway, I see a note about this removal here ( http://redmine.gromacs.org/issues/1346 ), though no reason is given. I'd suggest that you revert to a more functional version of gromacs ;)
> Hopefully I'm missing something and somebody else can point you to a better solution.

I think the behavior can be recovered with "direction" geometry, but that 
requires each half of the symmetric sampling windows to be set up separately, I 
think, rather than just a continuous vector like "position" used to provide. 
That's a shame if true.  It's a workaround, but it's much less convenient.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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