Re: [AMBER-Developers] ntb vs ifbox?

From: Yong Duan <>
Date: Sun, 04 Dec 2011 14:54:30 -0800

But, just because there are a few special folks that request such special
things, we should do it? What about the great majority of other users? For
those very few special folks, they have the freedom to edit prmtop.

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

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 12/4/11 2:17 PM, "Jason Swails" <> wrote:
>On Sun, Dec 4, 2011 at 2:46 PM, Yong Duan <> wrote:
>> Shall we force NTB>0 when IFBOX>0? There might be value of having two
>> controls for the developers. But for regular users and the community at
>> large, this probably causes a lot more problems than creating
>I don't think we should, since there may be instances in which people
>want to run a periodic simulation.  Also, how do we know what value of ntb
>to set?  (constant pressure? constant volume?)
>I could imagine printing out a warning in the output file or something,
>I don't think we should change that behavior.
>All the best,
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>AMBER-Developers mailing list
AMBER-Developers mailing list
Received on Sun Dec 04 2011 - 15:00:03 PST
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