AMBER Archive (2003)

Subject: shake problem?

From: Shuang Ding (sd517_at_nyu.edu)
Date: Mon Jun 09 2003 - 13:33:50 CDT

Dear Amber Users,

I tried to run a dynamic simulation of damaged DNA, using the similar protocol as DNA tutorial. The production stopped at ~50ps, and the two strands began to fall apart. But using the same protocol, the production of the unmodified DNA was still running.
Then I changed to heat up the system from 10k to 300k at constant volume gradually, then equilibrate the system at constant pressure and decrease the constraint on DNA gradually. The production stopped at 500ps production with error message: SHAKE cannot be accomplished. The temperature went up fast and the strands start to separated from the modified base during the final several snapshots. I checked the reflector and BLOWUP question part, and couldn't find some way to solve it.
Dose anyone has some suggestion? Thanks a lot.