From: Athreya, Nagendra Bala Murali (nathreya_at_illinois.edu)
Date: Wed Mar 01 2017 - 15:13:37 CST
I am planning to simulate a DNA translocating through a membrane under the influence of different electric fields applied in +z (highly positive field, Ex: 10 V) and -z (relatively lower positive field compared to the one applied in +z direction, Ex: 1V) directions simultaneously to see the effect it has on stretching the DNA. This is different than applying delta(z) in one direction. The potential at the membrane would be 0 and different potential gradient along +z and -z directions.
Since NAMD accepts only eField in the script, I thought of using TclBC Forces or GSMD or other available protocols to achieve this. I am unsure of how to actually specify these in the script and implement such a thing under an influence of eField.
I kindly request your help in solving this problem. Thank you for your time in advance.
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