On 17/08/2012 2:02 PM, shahid nayeem wrote:
Dear all
One basic clarification. How does LINCS algorithm influences the results
of final production run. In what respect a minimization, pr and final
simulation done with constraints = none and with constraint= all_bonds are
different.
Sounds like you should do some background reading on how and why
constraints work. Manual and refs therein are good starting points. Or
your favourite molecular simulation textbook. In a nutshell, you use
them in production simulation because they're a reasonable model and
allow a larger time step. You might avoid them when you're not yet at
equilbrium, because their implementation can be brittle when your
structure doesn't agree with the model physics.
Mark
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