[gmx-users] Pull code

[Justin Lemkul]

On 5/22/15 7:00 AM, Ming Tang wrote:
> Dear Justin,
>
> I want to simulate my triple helix using SMD, Can I use umbrella + distance?

Shrug.  Depends on what you're doing and trying to observe.

> I saw many people doing SMD simulation by fixing one end and pull another end
> in their journal. Besides, my triple helix deviates a bit from Z axis, but I
> do not know the angle. I checked both dim for distance and pull-vec for
> direction, and found both of them needs pull direction. If I set dim = N N Y,
> will the force-deformation be reliable?
>

Align with x using editconf -princ, then rotate to your heart's desire with 
editconf -rotate to align with whatever axis you want.

-Justin

-- 
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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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