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

Christopher Neale chris.neale at alum.utoronto.ca
Wed Apr 22 16:44:05 CEST 2015

Dear Justin:

I think you are correct. It may not even really be that much of a hassle though one may need to be very careful in system setup for umbrellas near the center of the bilayer when using pull_start=yes rather than pull_coord1_init (i.e., one may need to make sure that the solute COM is on the side of the bilayer that one specifies with pull_coord1_vec, though having not used it myself perhaps this is not even an issue?). Separately, I presume that pull_coord1_init=0 should be identical with pull_coord1_vec = 0 0 1 or pull_coord1_vec = 0 0 -1, though if I was using the new code that would be something I would check at the outset.

Dear Mahender:

Based on Justin's suggestion and your initial mdp file, you should try something like the following. I'm still using gromacs 4.6.7 so I can not verify the accuracy of your other parameters (or even be entirely sure about these ones, but they are worth a try).

;; Presuming that you start with the solute at +z relative to the bilayer and want to pull toward -z
pull        = umbrella
pull_geometry    = direction
pull_dim    = N N Y
pull_coord1_vec = 0 0 1
pull_coord1_rate = -0.002
pull_start = yes

;; I presume that 
;; pull_coord1_vec = 0 0 1 and pull_coord1_rate = -0.002 
;; is identical to
;; pull_coord1_vec = 0 0 -1 and pull_coord1_rate = 0.002 

;; I am not sure if pull_dim = N N Y is necessary, but I don't see how it could hurt.
;; Presumably the distance and the vector on which the pull_coord1_rate acts are already going to be entirely along z due to pull_coord1_vec , but I'd test that too if not using pull_dim = N N Y 

Please report back whether this works or whether you get strange behaviour when you hit the bilayer center.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: 22 April 2015 08:12
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

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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