Re: [AMBER-Developers] ntb vs ifbox?

From: Yong Duan <>
Date: Tue, 06 Dec 2011 19:28:10 -0800

That should work and, hopefully, not that many users are as innovative as
you are :).
But I like Dave's idea better.

Right now, sander quits when ifbox=0/ntp<>0/ntb<>0. We just need to
strengthen this by adding ifbox<>0/ntb=0 and make sure it is compatible
with the test cases (need to update the test suite).

Another thing that I often feel somewhat confusing is the ntx. I think the
manual and behavior are actually inconsistent. Sander takes the box
information at the end of restart, regardless of ntx, so long as ntb>0
(see ew_setup.f:load_ewald_info()). This is the desired behavior. But the
manual implies otherwise (there is also a typo), as if the user has the
freedom to choose to use the box information or not by setting ntx=7 or
ntx=5. In reality, they donšt. So, we need to update the manual to avoid
giving users false sense of freedom and empowerment :).

If above is true, ntx's function is pretty much limited to reading the
velocities (and formatted/netCDF restart files). But, irest controls the
use of velocities. Therefore, the only role that ntx plays is to
differentiate formatted or netCDF restart files. For this simple function,
it sounds awfully complicated to have so many useless choices.

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 12/6/11 4:37 PM, "Jason Swails" <> wrote:
>On Tue, Dec 6, 2011 at 6:23 PM, Yong Duan <> wrote:
>> Ah, so, it works if it was simulated/constructed as ifbox>0.
>> So the scenario is:
>> 1) construct a PBC system with IFBOX>0.
>> 2) simulate with NTB=0
>> 3) Then, simulation with NTB=1.
>> You could have said this earlier.
>I tried, just unsuccessfully :).  What do you think about my suggestion as
>far as providing a "smart" default while still maintaining the same
>behavior if users supply an explicit ntb value?
>What about other people?
>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 Tue Dec 06 2011 - 19:30:06 PST
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