Hello,
As far as I remember, the problem is quite more complex when NTP is used.
The coordinates are re-computed for the size of the box and the restraints
don't work anymore also.
It's a real (and long standing) problem when you try to equilibrate a
protein in solvent with some restraints on some positions and you want to
do several restarts with the restraints in place.
Gerald.
On Mon, Aug 8, 2022 at 10:46 PM Timothy Giese via AMBER-Developers <
amber-developers.ambermd.org> wrote:
> 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 Tue Aug 09 2022 - 02:00:03 PDT
