From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Tue Mar 16 2021 - 13:40:29 CDT
Dear Soumadwip,
This tutorial is doing potential map manipulation external to either NAMD or VMD. On page 3, point 6, they mention the external tools provided and how to compile them.
Best regards,
Dave
-- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Mar 6, 2021, at 2:13 AM, soumadwip ghosh <soumadwipghosh_at_gmail.com> wrote: > > 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 <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 >
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