Another option might be to leave the behavior as it currently is, except:
If iwrap=1 and ntr=1, then translate each molecule's input restart
coordinates immediately after reading the reference coordinates from
file (i.e., before the first energy evaluation) if the molecule's
average displacement from the corresponding reference coordinates is
more than 1/2 a box length.
On 8/8/22 8:29 AM, Carlos Simmerling via AMBER-Developers wrote:
> - you can use the restart file of the previous run as the inpcrd AND the
> refc. This works fine now, but I've never really liked the idea of
> continually changing what you call your "reference" structrure.
> - we could enforce iwrap=0 when using ntr=1 (but this can lead to
> coordinate overflow, especially for solvent)
> - we could shift the reference coordinates and save them to a "reference
> restart" file? seems too complicated.
> - we could skip translating atoms that have restraints applied? they aren't
> moving far anyway.
>
> other ideas?
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Received on Mon Aug 08 2022 - 07:00:05 PDT
