Re: [AMBER-Developers] ntb vs ifbox?

From: Yong Duan <duan.ucdavis.edu>
Date: Tue, 06 Dec 2011 15:23:47 -0800

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.

--
Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
530-754-7632
On 12/6/11 2:35 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>On Tue, Dec 6, 2011 at 5:17 PM, Yong Duan <duan.ucdavis.edu> wrote:
>
>>
>> Very good example, indeed!
>>
>> However, as far as I know, you can not simply change ntb from 0 to 1 to
>> realize this. You need box information that requires editing prmtop
>>and/or
>> restrt.
>>
>
>This example would work if the box info was there (i.e. via solvateoct or
>something).  ntb=0 means don't use the (existing) box info, ntb=1 means
>use
>the (existing) box info.
>
>All the best,
>Jason
>
>-- 
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
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Received on Tue Dec 06 2011 - 15:30:03 PST