I was unable to understand the actual intended meaning in David's post, but
I still think an error message would be good. If iwrap=1 is possible and
leads to unexplained crashes with restraints, then a sensible error message
would help the user. I'm not sure that avoiding iwrap=1 is going to solve
the problem in all cases... if not already, then at some point in the
future unwrapped coordinates are going to exceed floating point capacity.
If the suggested alternative is quite complicated, an error message could
always have an html link to a more detailed outline.
On Mon, Apr 3, 2017 at 12:37 AM, Sadegh Faramarzi Ganjabad <
safaramarziganjabad.mix.wvu.edu> wrote:
> Chris,
>
> Yes I used the same 'refc' file for both original and restart simulation.
> Actually, there is no option -ref in my submission script. When I was
> running the original simulation, it was complaining about not finding
> 'refc' file for restraints. Then I copied my input coordinate as 'refc' and
> put it on the same directory and ran simulations. However, when I try to
> visualize 'refc' on VMD it shows an abnormal structure (I don't know why)
> but the atom numbers and coordinates are there.
>
> I removed iwrap=1 and now the restart output structure looks normal.
>
> Thanks,
> Sadegh
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Received on Mon Apr 03 2017 - 00:00:03 PDT
