[gmx-users] reference group in constant velocity pulling, GMX 4

Simba Xiao simbaxiao at gmail.com
Fri Jun 5 04:13:28 CEST 2009

Dear all,

I am using the pulling code in gromacs 4.0.5 with constant velocity pulling.

My case is pulling protein in two opposite directions, which I do not want
any other extra force acting on the protein.

So I did not assign any reference group in the simulation, and I got a
warning saying that:  absolut coordinates is used as reference group and it
will cause artifacts.

According to the manual, ( 0, 0, 0 ) is used as reference group, but I still
do not understand what kind of artifacts could happen.

The only thing I can think of is the periodical boundary, but I am not sure,
could any one have any idea?


Senbo Xiao

PICB, Shanghai, 200031
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