[ADF-LIST] Bond boost output values

Alexei Yakovlev yakovlev at scm.com
Tue May 18 12:17:30 CEST 2021

Dear Brandi,

In ams, the coordinates "boosted" by the bond-boost are printed to the 
output file, for example as:

  Step: 77500
  Chain: C.t O H O C @1 @4
  Atoms: 614 596 15 616 613 614 616
  Length:         11.420
Created distance restraint 614 596 at 1.300 A, fc=.030
Created distance restraint 614 616 at 2.500 A, fc=.050
Created distance restraint 614 613 at 1.300 A, fc=.050
Created distance restraint 15 616 at 1.000 A, fc=.050
Created distance restraint 616 613 at 1.300 A, fc=.050

The fort.* files are specific to the reaxff program, which should not be 
confused with the Reaxff engine used by both programs, reaxff and ams. 
The latter writes results to the ams.rkf file in the results directory 
and to text output files such as out and logfile.

Kind regards,

Alexei

On 17/05/2021 21:48, Brandi Ransom wrote:
> Hello there,
>
> I’m a PhD student at Stanford working with polymers and was hoping 
> someone on this list has had experience with the bond boost feature in 
> ams 2020 suite. I am specifically working within the ReaxFF module, 
> but would be happy to hear about your experiences using any other module.
>
> I am familiar with bond boost in the ams 2019 suite, where it outputs 
> many different fort.## files, and I was hoping to find the equivalent 
> information from running bond boost in the ams.2020 suite.
> As of now I can see in the 2020 output file there are the different 
> energies at specific time steps, and which atoms are being selected 
> for boosting.
> In ams2019, the fort.76 file also tracked the distance between the 
> boosted atoms and the restraint energy, which I haven’t found in the 
> 2020 suite.
>
> *Does anyone know if these values can be accessed anywhere? And any 
> other values or analysis tools you have found helpful when using bond 
> boost? *
>
> Thank you,
> Brandi Ransom
>
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