[gmx-users] Orienting molecule in a correct direction

[faride badalkhani]

Dear all,

I want to define z axis as the reaction coordinate in a series of umbrella
sampling simulations. As a first step, I use the editconf -prince to orient
the ligand along the x axis and then I change the x and z columns in an
editor. But, every time I get error at pulling step. Could you tell me what
is wrong?
Any help is appreciated.

Regards,
Farideh