[gmx-users] pull code absolute reference

bv07ay bv07ay at brocku.ca
Wed Aug 18 17:45:55 CEST 2010

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                        = 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?

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