[gmx-users] Problem using trjconv and g_potential

Manik Mayur manik.mayur at gmail.com
Tue Apr 13 08:01:34 CEST 2010


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

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


Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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