Hi Chris,
FYI, I have seen similar problems for several systems now, which were
indeed due to atoms not being in the same image in the unit cell.
Currently, I 'solve' this by adding an "autoimage" step before restarting
in my job submission scripts.
That works, but a solution in the code would be nicer/clearner, of course.
Thanks,
Marc
On 31 March 2017 at 17:30, Chris Neale <candrewn.gmail.com> wrote:
> Sadegh: are you sure you used the same input for -ref in the original run
> and the restart? Also, that your restraint mask was the same in both runs?
> I'd also suggest taking a look at your -refc input... are any of the atoms
> in restrained groups wrapped around PBC (i.e. not in the same image in the
> unit cell) in that file?
> 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.
>
>
> 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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Received on Fri Mar 31 2017 - 10:00:03 PDT
