Re: [AMBER] solvatebox

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Tue, 7 Dec 2010 10:26:36 -0800

> I want to have a water box with following conditions:
> water model = TIP3P
> distance between the solute and wall of the box = 8 angstroms
> number of water molecules = 7400
> box type = cubic
> box length = 62 angstroms
> How I should use solvatebox for obtaining them?

8A is realistically too small for a good simulation.
It sounds like you are trying to replicate someone else's setup,
which may be all but impossible if your solute coordinates differ
from theirs. Even with the same coordinates, it may be hard to
get the same number of waters and the exact same box length; you
might have to try repeatedly with cutoff of 8, 8.001, 7.999, etc.
each time restarting leap to get a fresh setup. Due to all the
above, I would think twice about what you are trying to do.


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Received on Tue Dec 07 2010 - 10:30:06 PST
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