Re: AMBER: error due to exceeding left-hand side digital numbers in restart output

From: David A. Case <case.scripps.edu>
Date: Mon, 18 Jun 2007 11:06:16 -0700

On Mon, Jun 18, 2007, Cenk Andac wrote:
>
> I have been running a 300 ns MD for an RNA hairpin solvated by TIP3
> waters. somewhere around 50 ns of MD , I seem to get some errors with
> restart files so that the next sander routine does not start. After
> going through the coordinates in the previous restart file, I have
> noticed that some coordinates were filled with lots of stars, like
> ****.******* , instead of numbers.

There is not much you can really do here. Back up to the last good restart
file, and start again, setting iwrap=1 in the sander input. Going to netcdf
trajectory output would also eliminate this problem, but I think most people
(including me!) have been slow to make the change to the new format.

...regards...dac

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Received on Wed Jun 20 2007 - 06:07:24 PDT
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