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

[Sajeewa Pemasinghe]

Thank you very much. I really appreciate it.

On Sun, Mar 26, 2017 at 6:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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