[AMBER] How to calculate velocity in steered simulation

From: Pinky Mazumder <pmazumder67.gmail.com>
Date: Fri, 24 Jul 2020 22:58:05 -0500

Dear Amber Users,

Hope you are doing well.

How to calculate the velocity in steered molecular dynamics simulation?
https://ambermd.org/tutorials/advanced/tutorial26/section1.html is the
tutorial I am following.

Please help me out. I need to plot the Force vs extension curve from the
outputs. I am using the formula F=k(vt-x) and vt=extension. But I do not
know if the way I am calculating the velocity is correct or not?

Could you guys please help me out?


Pinky, Sharmi
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Received on Fri Jul 24 2020 - 21:00:04 PDT
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