[gmx-users] g_select position variables

Cara Kreck cara_a_k at hotmail.com
Tue Jul 29 05:18:30 CEST 2014

Hi everyone,

Is it possible to use a position variable in conjunction with x,y,z keywords in g_select?

I'm trying to select all molecules within a channel embedded in a membrane. In case the protein and/or membrane moves around I want to use position variables instead of numerical values to define the z range. I've tried this in my selection.dat file:

solution = resname SOL or resname CL;
top = res_com of resnr 1181;
bottom = res_com of resnr 55;
cavity = solution and z bottom to top;

cavity = solution and z<top and z>bottom;

But I get an invalid selection error. However, if I substitute top and bottom with numbers, it does work. Is there something wrong with my syntax or am I just trying to do the impossible?




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