If you want to pull along a vector which connects to groups, the easiest way is to run 'g_dist' over your starting *.gro file. this measures the distance and the vector connecting both groups. From GROMACS-4.0.x you don't need to normalise the vector. So you can directly use this vector.
greetings
thomas

Thanks for ur suggestion Justin,

I'm facing trouble in setting that vector, actually I cant figure out how
can i set up a vector. Is there any easier way with which i can set up a
vector. Thanks

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