From: Jun Zhang (coolrainbow_at_yahoo.cn)
Date: Wed May 18 2011 - 20:29:07 CDT
I am going to perform some SMD simulations but I have two choices: one by direct SMD configuration in NAMD or manually configured in a script by tclForces. Although the latter is more flexible, I wonder if the tcl script in every time step will slow down (obviously?) the total speed of MD since my system is quite large? Maybe direct SMD will be faster since it is implemented in C++? Any suggestions will be appreciated.
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