[gmx-users] pull code absolute reference

[Justin A. Lemkul]

bv07ay wrote:
> Hello,
> i am having trouble using the pull options in gromacs 4.0.4.  i am 
> simply trying to move a protein from the top of the box to a certain 
> point in the center.  i have had no luck using a constant pulling or 
> umbrella pulling the error i receive is:
> 
> "You are using an absolute reference for pulling, but the rest of the
>   system does not have an absolute reference. This will lead to artifacts."
> 
> here is my most recent .mdp pull options:
> 
> ; PULL
> pull                        = umbrella
> pull_geometry                = position
> ;pull_group0                =
> pull_init1                = 3.279 3.279 3.90
> pull_group1                = MID
> pull_dim                = Y Y Y
> pull_k1                        = 50
> 
> 
> is there a way to make my system have an absolute reference? or is there 
> some other way of pulling it that has worked for others?
> 

The error message is related less to the pull options than it is to COM motion 
removal.  For instance:

http://lists.gromacs.org/pipermail/gmx-users/2009-April/041329.html
http://lists.gromacs.org/pipermail/gmx-users/2006-July/022753.html

If you search the mailing list archives you will find lots of related posts.  I 
pulled those up immediately by searching: "absolute reference" pulling.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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