AMBER Archive (2009)

Subject: [AMBER] MD simulation with a partially flexible system

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Tue Feb 17 2009 - 08:38:10 CST


Dear amber users,

    I'd like to perform a microsecond-scale MD simulation to see the change of a subdomain with time. So it is necessary to reduce the computational expense by keeping only the subdomain and its surrounding atoms to move while keeping the rest of the system as rigid body during the course of simulation. I checked the amber mannual and didn't find a good choice.
Does anyone know whether this job can be done in AMBER package?

Thanks very much.

------
Jeffrey

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