Thank you Daniel.
I like the informative error message solution. As long as people know what
to do the code doesn't need to do it for them.
On Fri, Mar 31, 2017 at 10:57 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Mar 31, 2017 at 12:30 PM, Chris Neale <candrewn.gmail.com> wrote:
> > If the issue is simply PBC wrapping during the run then that sounds like
> > something that should get fixed in the code at some point, esp given that
> > it's called a "restart" file.
>
> An internal solution here is not so simple. I don't see an easy way
> you could have the code realize that your system has been imaged with
> respect to the reference you've given it. I guess you could have it
> detect a very large restraint energy and then do the equivalent of
> 'autoimage' to the coordinates and see if that helps, but that's a lot
> of code duplication and may not always be the correct thing to do. The
> solution may be to make sander/pmemd output a more informative error
> message when restraints and iwrap are on.
>
> Another alternative is when using positional restraints turn iwrap off
> and use netcdf trajectories and restarts. However, in my opinion the
> easiest thing to do is make sure you autoimage your restarts when
> using position restraints.
>
> -Dan
>
> >
> >
> > On Fri, Mar 31, 2017 at 12:58 AM, Marc van der Kamp <
> > marcvanderkamp.gmail.com> wrote:
> >
> >> Hiya,
> >>
> >> You can try reimaging your restart file (with ccptraj) before
> restarting.
> >> It may be that molecules involved in the restraint are in different
> >> 'images', which can lead to the behaviour you see upon restarting.
> >>
> >> Marc
> >>
> >> On 31 Mar 2017 06:23, "Sadegh Faramarzi Ganjabad" <
> >> safaramarziganjabad.mix.wvu.edu> wrote:
> >>
> >> > Hi Chris,
> >> >
> >> > I turned off restraints and it works! it's weird. Do you know how I
> can
> >> > restart my simulations without having to turn off restraints?
> >> >
> >> > Thanks,
> >> > Sadegh
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>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Fri Mar 31 2017 - 10:30:02 PDT
