[AMBER] removing center of mass

From: Bala subramanian <bala.biophysics.gmail.com>
Date: Tue, 17 Mar 2009 15:21:28 +0000


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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Received on Wed Mar 18 2009 - 01:16:53 PDT
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