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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 20 2007 - 06:07:24 PDT
