Re: [AMBER] The recommended way to create periodic box around lipid bilayer system ?

From: David A Case <>
Date: Mon, 1 Jul 2013 12:12:54 -0400

On Mon, Jul 01, 2013, Marek Maly wrote:

> I am just curious if there is any recommended approach
> how to create periodic box around solvated (externally)
> lipid bilayer system.
> I obtained using "setbox UNIT vdw" (I used "set UNIT box { X Y Z }"
> command in the final step).

I personally don't think that setbox UNIT vdw is every very useful; the second
form above is probably what you want, but of course you have to do some visual
or other investigation to obtain good values for X Y Z.

> Let's just notice that during the minimization phase the system was
> maintained in a good
> box, the problem with wrong reimaging starts from the NVT MD.

Do you somehow have iwrap=1? You probably want to have no reimaging for these
sorts of simulations. (Although, aside from visual appearance, it should
work; nevertheless, I'd recommend avoiding it.)


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Received on Mon Jul 01 2013 - 09:30:02 PDT
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