[gmx-users] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

[Justin Lemkul]

On 3/26/17 8:11 AM, Sajeewa Pemasinghe wrote:
> Hi all,
>
> I have a system in which I need to maintain the center of mass distance
> between two molecules constant for an umbrella window. The structures are
> not strictly aligned along an axis as they are the product of an
> equilibrium simulation.I have the following code.
>
> pull = umbrella
> pull_ngroups = 2
> pull_group1_name = molecule1
> pull_group2_name = molecule2
> pull_coord1_type = umbrella
> pull-geometry = distance
> pull_coord1_groups = 1 2
> pull-dim = Y N N
> pull_coord1_rate = 0.0
> pull_coord1_k = 2000
>
> I have the following questions.
>
> 1) Does pull-dim = Y N N mean that the k=2000 is applied along the x
> coordinates only in maintaining the distance constant?
>

Yes.

> 2) If I want to apply a harmonic potential to maintain the distance along
> both x and y axis constant (in maintaining the distance *r* constant) do I
> have to make the following changes?
>
> pull_coord2_groups = 1 2
> pull-dim = Y Y N
> pull_coord2_k = 2000  # this is applied on the y coordinate (that is the
> picture I have in my mind)
>

No.  You have one biasing potential that acts along x and y.  The biasing force 
is applied based on the distance calculated along those two axes, not 
independently in x and y.

-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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