On Wed, Jul 22, 2020, DHEERAJ CHITARA wrote:
>
>The default distance for solvent box from the solute molecule is 8 Angstrom
>as recommended by amber.
??? Where did you find this? As far as I can see, the solvateBox command
in tleap requires the user to provide a buffer size, and there is not a
default. (But I could be wrong, and maybe there is documentation that
needs fixing..) In any event, 8 Ang. is not a "recommended" value,
certainly not in 2020, with today's more powerful computers. Values like
12 or 14 Ang are more "normal", and some systems may require even larger
values.
>
>But, Can I set the distance as 2 Angstrom or 3 Angstrom between solute and
>solvent box.
My short answer is "Why would you want to do this?"
Go ahead and experiment, but I'm not sure how one would use the resulting
system. You would have a periodic system with the solutes exceedingly
close to each other. That's a bit like a very high concentration, except
that the periodic conditions would prevent the solutes from every actually
meeting, unless the solute conformation changes enough from its initial
state.
...dac
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Received on Wed Jul 22 2020 - 12:30:06 PDT
