[gmx-users] Translational Pulling

[Justin Lemkul]

On 4/22/16 3:51 PM, Ray Chao wrote:
> H
> ​i, Justin,
>
> Actually I was using freeze groups together with pulling. However, the
> atoms seemed to be frozen and weren't pulled away at all. Following is my
> mdp file:
>
> freezegrps               = X  Z
> freezedim                = Y Y Y Y Y Y
>
> pull                           =  umbrella
> pull-geometry         =  distance
> pull-dim                   =  N N Y
> pull-ngroups            =  2
> pull-group1-name   =  X
> pull-group2-name   =  Z
> pull-coord1-groups =  1   2
> pull-coord1-rate       =  -0.01  ;velocity 0.01 nm/ps
>
> I also tried to used constraints pulling, but it gave an error of "The pull
> constraint reference distance for group 0 is <= 0".  What change do I need
> to make to make the group X and Z approach each other?
>

You can't freeze both groups and try to move one.  If you want the position of 
one group fixed, then freeze it and pull the other towards it.  Freezing and 
trying to impart motion are mutually exclusive.

-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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