AMBER Archive (2003)

Subject: restart MD

From: Shuang Ding (sd517_at_nyu.edu)
Date: Tue Jun 10 2003 - 13:12:08 CDT

Dear Amber Users,

I am doing a simulation of the carcinogen damaged DNA. The system blow up after 500ps production because of the shake problem. Then I try to restart the MD from 400ps. The coordinates and box size are read from 400ps restrt file when restart, the starting velocity is dependent on the random number. The restart MD run to another 500ps now. Is it a valid technique for DNA simulation?
Thanks a lot for your help.