AMBER Archive (2003)

Subject: Re: AMBER: machine dependent?

From: Shuang Ding (sd517_at_nyu.edu)
Date: Tue Aug 12 2003 - 13:48:00 CDT

Dear Dr. Michael,
Thanks so much for your detailed explanation. It really helps me to understand more about SHAKE. I had a strained base adduct which has an unsaturated bicyclo[3.3.1]nonane type ring system. If I turn SHAKE off, what time step should be used?
When the SHAKE failure occurred, I went back in the trajectory before SHAKE failure, and restarted the MD with reassigned velocity. For example, the SHAKE failure occurred at 500ps, I reassigned the velocity at 400ps where the trajectory was stable and restarted it, then the system continued for another 1.5ns till another SHAKE failure, I restarted at 1.4ns, and the system ran for another 1ns. In this way I got a total 4ns trajectory, and the rmsd of this pieced trajectory looks reasonable. What do you think of such a trajectory?

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