Hi, I have a slab geometry configuration with water and some ions. I wish to extract the charge/potential distribution due to ions in the center of my box. For this I used trajconv to have a box of required dimensions and center the required ions in it. And then run g_potential on it to get the charge and potential distribution. But the g_potential fails with a segmentation fault. I am producing the steps followed by me below so please suggest me where could I have gone wrong.
1) My actual box dimensions are 4 X 5 X 30. I first use trjconv to center my ions in a box of dimensions 4 X 5 X 10 (I am sure all of them will fit in here upon centering): trjconv -f Sim_ions.trr -o Soln.trr -s Sim_ions.tpr -n Sim_ions.ndx -b 1000 -box 4 5 10 -center 2) Select group: Ions (for both centering and output) 3) Use g_potential to plot the charge distribution and the potential distribution- g_potential -f Soln.trr -s Sim_ions.tpr -n Soln.ndx -o potential.xvg -oc charge.xvg -d Z Selected 4: 'Ions' trn version: GMX_trn_file (single precision) Reading frame 0 time 1000.000 Dividing the box in 10 slices Segmentation fault Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA
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