[gmx-users] How to set up constraint distcance pulling

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 7 13:59:27 CEST 2012

On 6/7/12 7:38 AM, xiaowu759 wrote:
> Dear gmxers,
> I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of
> distance between the COMs of two molecules. However, quite strange resuluts are
> generated, i.e., the distance can not be fixed at the value defined by
> pull_init1. The pull opinions are given below. Could you please tell me how to
> deal with this? Thanks a lot for any reply.

How far away from the target value are the results in terms of COM distance?

> Chaofu Wu
> ;Pull opinions
> pull = constraint
> pull_geometry = distance
> ;pull_dim = Y Y Y

The comment here has no effect; pull_dim defaults to "Y Y Y."

> pull_group0 = r1
> pull_group1 = r2
> pull_nstxout = 0
> pull_nstfout = 5
> pull_init1 = 0.80

How does this pull_init1 value compare to the COM separation in the coordinate 
file?  If the distance is not very close, the constraint algorithm may fail.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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