AMBER Archive (2009)

Subject: [AMBER] removing center of mass

From: Bala subramanian (
Date: Tue Mar 17 2009 - 10:21:28 CDT


1) I simulating a DNA molecule with igb=1. I would like to know if i need to
change the nscm from default (1000) to remove trans. and rotation of center
of mass. How much can i keep for GB simulation. Any suggestion based on
your experience will be highly helpful to me.

2) What should be the intdiel for nucleic acid simulation with GB. In
literature i am seeing both 1.0 and 2.0 used for internal dielectric.

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