Re: [AMBER] Solvate box

From: M. L. Dodson <>
Date: Wed, 26 Jan 2011 18:04:51 -0600

On Jan 26, 2011, at 5:52 PM, Bill Ross wrote:

>> You will probably have to set a box considerably larger than what
>> packmol thinks you need. The reason is that you will get VDW overlap at
>> the edges of the boxes you construct. Constant pressure dynamics is
>> your friend (it is needed to equilibrate the density). If NPT dynamics
>> continually bombs, increase the size of the initial box manually until
>> it runs. Plot the density so you can convince yourself it is
>> equilibrated.
> I thought the initial box dimensions would be chosen by leap's setbox,
> so if there's a problem, it would seem to be a bug in leap. Unless a
> feature has been added to loadpdb to pick up some box record from the
> pdb file.
> But when I wrote setbox, I believe I had it using the outside of the
> vdw shell to draw the box, so I'm puzzled that there would be vdw
> overlap.
> NPT for sure in any case :-)
> Bill

No, you are correct, but there is a density calculator on the packmol
page that will estimate box dimensions. What I meant was that the
box size it suggests will give you a box which will have VDW overlaps
when you tile them. You need a vacuum buffer around the box.

The box needs to be (surprisingly) larger than expected (in my
experience). What I meant was that if the dynamics crashes, you
don't have to start over, just edit the box dimension in the input
coordinate file.

M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Wed Jan 26 2011 - 16:30:02 PST
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