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

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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