From: soumadwip ghosh (
Date: Mon Mar 01 2021 - 03:13:50 CST

Hi folks,

I am following modelling nanopores for DNA sequencing tutorial in NAMD.

I have done steered MD simulation of DNA+mspa to calculate the average
electrostatic potential of the system. However, we need to add the applying
external field (120 mV in this case) to get the complete electrostatic
potential. It is also the first step to study accelerated translocation
(grid-steered MD) of DNA through the pore under applied external field. I
am applying the following command (written by Jeff Comer) in this wonderful

./grid/gridExternalForce electric_raw.dx 0.02585 1.2 electric.dx .

But it is not working since the script is a .C script (error: bash:
./grid/gridExternalForce: No such file or directory) and I am unable to
compile it properly. Can you help me troubleshoot this? I tried using gcc
for compilation but to no use.

Also , in the grid directory I did see a gridExternalField.C
and thirdForce.C but no utility such as gridExternalForce to execute. I
obtained the scripts from the zip file that was provided with the tutorial.

I will be obliged if someone helps me out.

Soumadwip Ghosh