AMBER Archive (2008)

Subject: Re: AMBER: Query on restart file

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 30 2008 - 21:03:53 CDT

we need more info- is it possible that you did not have wrapping on
for a periodic simulation, and the coordinates got too large? there is
lots of info in the archives on that, check iwrap.

On Thu, Oct 30, 2008 at 9:49 PM, Neha Gandhi <n.gandhiau_at_gmail.com> wrote:
> Hi Amber community,
>
> I ran 17 ns of production runs (each trajectory file consist of 500 ps with
> 50 frames). I tried to run another 500 ps after 17ns but it just says cannot
> read coordinates from the previous .rst file. When I checked , there is no
> spelling error and I checked the previous rst files. To verify I again run
> the 16th ns md again and no issues with it. Only thing I cannot further run
> MD after 17th ns? What could be the problem and the possible solution? I m
> following the mm-pbsa tutorial in amber.
>
> Many thanks,
>
> --
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
>
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