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
--
========================================
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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