Re: [AMBER-Developers] ntb vs ifbox?

From: Jason Swails <>
Date: Sun, 4 Dec 2011 20:29:23 -0500

On Sun, Dec 4, 2011 at 5:54 PM, Yong Duan <> wrote:

> But, just because there are a few special folks that request such special
> things, we should do it?

If it doesn't overly-complicate things for normal users, I think yes.

What about the great majority of other users? For
> those very few special folks, they have the freedom to edit prmtop.

I don't think we should start encouraging people to modify that file by
hand. A hand-edited prmtop file is a recipe for ugly, obscure errors by
even the most experienced prmtop hackers.

Force field stuff, IMO, belongs in the prmtop (IPOL, SCEE/SCNB, etc.). I
don't think PBC falls into this category.

It's so easy to mess up now. If one accidentally sets wrong ntp, you'd

ntb or ntp? IFBOX is only enough to tell us, usually, whether ntb == 0 or
ntb /= 0, not whether ntp == 0, ntp == 1, ntp == 2, ntb == 1, or ntb == 2,

have to restart. I bet a lot of people run into this. I did, numerous
> times. And, I've never come to the occasion of needing ntb=0 with IFBOX=1
in my ~20 years of using AMBER. Why one builds a periodic box and runs
> non-PBC? To study surface-tension effect to find out how a box of water is
> gradually squeezed into a sphere? I guess, there are people who do that.
> But, for great majority of our users, I bet when they build a IFBOX=1
> system, they meant to run simulations with ntb > 0 and when they build
> IFBOX=0 system, they meant to use it for ntb=0.

I still think the choice of periodic boundary conditions and their
parameters should be deliberate. Furthermore, the default ntb is 1, (NVT).
 If you try to set a GB model with that, you get a helpful error message.
 Likewise for trying to use PME with ntb==0.

What I could see us doing, though, is to make the default value
IFBOX-dependent. For instance, if IFBOX==0, then ntb==0 is the default,
but if IFBOX /= 0, we stick with ntb==1. If a user manually provides an
ntb value, we just use that. Anything more than that is overreaching IMO.

We would also be breaking long-standing behavior, so I think there should
be a very clear gain for such a break with tradition (such as enabling
mixed scaling for GLYCAM+AmberFF for SCEE/SCNB --> prmtop and avoiding the
ridiculous-ness of IPOL=1 for a fixed-charge FF).

Just my 2c (Fighting inflation).

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Sun Dec 04 2011 - 17:30:02 PST
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