AMBER Archive (2006)

Subject: AMBER: A question about Dynamics.

From: Qingning Shu (
Date: Mon Sep 18 2006 - 15:40:21 CDT

Dear Amber Users:
I have a question about dynamics. I have a system. In Equilibration step I used cartesian restraint on the residues that are far away from active site. What shuold I do in the production MD, maintain the restraint or remove it? I thought I should keep it and ran the preoduction MD with the restraint. But I found in the potential-Vs-time plot the potential energy suddenly dropped at the beginning point of production MD. In other words, the potential energy was not continuous at that point. I Ran it with generalised Born solvation (igb=1) in amber8. Is there anyone can help me? Thank you in advance.

Have a nice day.


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