[gmx-users] g_select problem

Albert mailmd2011 at gmail.com
Wed Aug 21 16:13:28 CEST 2013


  I am trying to calculate the number of water molecules within 3 A of a 
resid 51, and here is my command:

g_select -f md.xtc -s input.pdb -os water.xvg -sf selection.dat

here is my selection.dat:

waterO = name "T3P" and name O;
close = waterO and within 0.3 of resnr 51;

the command run without errors, but I noticed that the number of water 
molecules in the output file are all 0. When I visualize each frame, I 
observe a lot of water molecules within the defined region.

Does anybody have any idea what's the problem?



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