[AMBER] Steered MD with highly charged species

From: Delwakkada Liyanage, Senal Dinuka <sdd313.msstate.edu>
Date: Tue, 9 Jun 2020 15:55:06 +0000

Hello Amber Users and Developers,

I am attempting to simulate an unbinding of a porphyrin (charge +4) from a G-quadraplex structure. Since I am fairly new to this approach I followed the tutorial for ASMD and obtained a PMF curve at 10 A/ns pulling speed. But I realized that my ligand is highly positively charged and the PMF would obviously keep rising due to Coulombic forces. I would highly appreciate your experienced insight on handling such situations. My inputs were the same as was suggested in the Amber Tutorial 26. I have amended my resulting PMF curve as well.

Thank you

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(image/jpeg attachment: PMF.10_100.25tps.jpg)

Received on Tue Jun 09 2020 - 09:00:04 PDT
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