[AMBER] Positional restraints

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 13 Nov 2013 17:41:50 -0300

Hi everybody,

I'm simulating a system in which there is a conserved water molecule in the binding site of the protein. I used restraint_wt=1.0 during energy minimization, restraint_wt=0.1 during heating and density equilibration. This resulted to the water molecule flying out of the binding site.

It's obvious that I should had used stronger restraints. Is there a rule of thumb as to the range of restraints that one should use during minimization, heating and density equilibration? Should there be a gradual relaxation of restraints before production MD?

Thanks in advance for any advice



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Received on Wed Nov 13 2013 - 13:00:02 PST
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