From: soumadwip ghosh (soumadwipghosh_at_gmail.com)
Date: Sat Mar 06 2021 - 02:12:11 CST
Hi folks.
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
have followed the NAMD tutorial below:
http://bionano.physics.illinois.edu/sites/default/files/nanopore-protocols.pdf
. I am applying the following command:
../grid/gridExternalForce electric_raw.dx 0.02585 1.2 electric.dx (you can
find the procedure on page # 25 of the tutorial attached) . But it is not
working since the script is a .C script and I am unable to compile it
properly. Have you run this utility before and help me troubleshoot this? I
tried using gcc for compilation but to no use.
Could someone provide some insights into how to make it work?
Soumadwip Ghosh
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST