[gmx-users] steered MD

Kamil Khafizov khafizov at sissa.it
Thu Mar 2 11:39:10 CET 2006

Dear all,

I was trying to pull a ligand from a protein using AFM pulling option of 
Gromacs 3.3 but seems to be that it does not care about parameters that I 
specify in pull.ppa file. In particular, in spite of the fact that I may 
write to the input file coordinates of the unit vector describing the 
direction of pulling, gromacs does it in its own way in the direction of axis
connecting centers of mass of reference and pulled groups AND not in the 
direction indicated in *.ppa file. I tried also do not indicate the 
reference group, thinking that it may work if pulling will be in absolute 
coordinates but I failed again because program just connected center of 
mass of the pulled group and point with coordinates (0 0 0)..
Does someone know how to make it working?


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