Re:Re: [AMBER] cutoff

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sat, 5 Jun 2010 15:21:31 -0700

> what I study is doing MD simulation of EGFR in complex with
> an inhibitor, so is cutoff of 8 angstrom enough? Or 10 is better?

This is still not enough info. However I have reached a conclusion :-)
I recommend using 8A to do an initial study, while you learn in order
to make your own decision down the road. 8A will enable you to learn
faster. If you also do a 10A short simulation you will know what the
time difference is and will know half of what is at stake. The other
half is the scientific issue, depending on how much simulated time
you plan to run (longer implies longer cutoff, but I don't know what
the time scales are for such decisions).


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Received on Sat Jun 05 2010 - 15:30:05 PDT
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