[gmx-users] gmx make_ndx - separating pulling groups by fragments

vprytkov vprytkov at uci.edu
Tue Oct 4 05:33:17 CEST 2016


Hello! I'm trying to conduct a pulling simulation with two identical 
proteins and centers of mass distance being the reaction coordinate. 
They are distinguished by fragment index in vmd (0 and 1), but the 
residues in the .gro file run from 1 to 178 and again from 1 to 178. How 
to I used make_ndx command to create an index file for the pulling 
simulation?
Thank you!


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