[gmx-users] Gromacs 2016 pull options

[Justin Lemkul]

On 2/20/17 8:09 AM, Gmx QA wrote:
> Dear list
>
> Could someone please clarify a few issues I have with the 2016 version of
> the pull code. Or rather, explain why the below approach is not working.
>
> I am trying to pull a small molecule though a bilayer. Initially, the drug
> is "below" the membrane, i e has a smaller z-coordinate, so I want to pull
> in the positive z direction through the membrane.
>
> The following is a snippet of my mdp-file, with the relevant parts for the
> pull specs.
>
> pull                      = yes
> pull-ngroups             = 2
> pull-ncoords             = 1
> pull-coord1-groups       = 1 2
> pull-group1-name         = drug
> pull-group2-name         = membrane
> pull-coord1-type         = umbrella
> pull-coord1-geometry     = direction-periodic
> pull-coord1-vec          = 0 0 1
> pull-coord1-rate         = 0.1
>
> This I think should define two pull groups,one for the drug and one for the
> membrane, and it should pull the drug molecule with pull-coord1-rate in
> positive z. I am using direction-periodic since I expect to pull more than
> half the box z length.
>
> When I test this, running a 1 ns simulation, during which I expect the drug
> to be pulled a significant way, nothing really happens with the com of the
> drug, it just "sits" out in the water phase.
>

You didn't set a value of pull-coord1-k, so it defaults to zero and therefore 
you get no biasing potential.

http://manual.gromacs.org/documentation/2016.2/user-guide/mdp-options.html#com-pulling

-Justin

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

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

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