Re: [AMBER] WaterBox is getting distorted while running PMF

From: David Cerutti <>
Date: Fri, 16 Aug 2019 13:10:56 -0400

What do you mean by 'distorted?' Is the ratio of box lengths changing? If
so, then make sure to set the barostat to do isotropic rescaling, ntp = 1,
not ntp = 2 or 3. If the system appears to be moving out of the water box,
this is just the periodic boundary conditions at work, and you can make the
result look pretty by centering the wrapped box on the centroid of your
system. If the water content of the box seems to be developing cavities or
looking like a block of swiss cheese at the corners, then this is likely
the result of not equilibrating the volume under ntp in the first
place--the system is forming a vacuum bubble (one, not many even though it
may look like many if the bubble occurs on an edge or corner of the box).


On Fri, Aug 16, 2019 at 12:18 AM Airy Sanjeev <>

> Hello Amber User,
> I am doing potential of mean force calculation for dimer structure using
> umbrella sampling method. While running the production run, the waterbox is
> getting distorted. I have used iwrap command but even then the waterbox is
> not properly oriented. Kindly help in this regard.
> Thanking you in advance
> --
> with best regards,
> *Airy Sanjeev, PhDPost Doctoral Fellow*
> *Indian Institute of Technology Guwahati, Guwahati*
> *Assam-781039, India*
> _______________________________________________
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Received on Fri Aug 16 2019 - 10:30:02 PDT
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