Re: [AMBER] Solvate box

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 26 Jan 2011 15:52:00 -0800

> 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

NPT for sure in any case :-)


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Received on Wed Jan 26 2011 - 16:00:03 PST
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