[gmx-users] Calculation of Electrostatic Potential at a Nanotube

Bob Johnson robertjo at physics.upenn.edu
Wed Oct 25 00:29:44 CEST 2006

Hello everyone,
I am trying to calculate the electrostatic potential at the surface of a carbon
nanotube from an MD simulation involving water and other adsorbates binding to
the nanotube. Since the nanotube atoms are uncharged this is how I was

1. I computed the trajectory using the normal force fields
2. I then went and altered the nanotube topology file and gave each carbon atom
a fictitious charge of 0.1
3. I then used the rerun feature to recalculate the electrostatic energy between
the nanotube and water (for example)
4. The average electrostatic potential is this energy divided by the total
nanotube charge

However, it seems that my results (e.g. the sign of the potential) does not
agree with some preliminary calculations I did where I calculate the potential
via brute force summing q/r. One thing that I'm concerned about is that the
total charge of my system when I use mdrun -rerun is non-zero since I'm giving
the nanotube atoms a charge. Will this effect the calculated electrostatic

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