AMBER Archive (2001)

Subject: weights for DNA and ions

From: Raja Swaminathan (rajaamber6_at_rediffmail.com)
Date: Wed Feb 21 2001 - 03:24:22 CST

hi
i am doing MD on a DNA duplex. in the first stage of minimization weights are given only to DNA (amber tutorial) and not the ions. does it cause any problem because equilibration of water may take away the ions out of the scene.

is it advisable to constrain both DNA as well as ions in the first stage itself

thanks
raja

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