Hello,
first, make sure that your rst-file is not corrupted: Try e.g. to create
a pdb file from it using the ambpdb tool, but also have a look into the
file.
Second, ensure that your input file reflects the restart intention (see
the Amber manual for details). Try a short test calculation and restart
it, to see that all your input parameters are correct.
Finally, you provided only sparse information about your specific
problem: "simulation could not restart" is not very descriptive.
Regards,
Anselm
Am 02.05.2013 03:53, schrieb 纪晓峰:
>
> Dear All
> I need to restart a molecular dynamics calculation that was stopped due to a
> power outage.
> I tried to restart the simulation by the command line :
> pmemd.MPI -O -i md.in -o md_new.out -p lip.prmtop -c md.rst -r md_new.rst -x
> lipase_new.mdcrd -ref md.rst -inf md_free_new.info
> where md.rst is the rst file, which was saved before the computer was
> powered off.
> but the simulation could not restart. maybe there were some problems in the
> md.rst.
> At the same time, during the whole simulation, the parameter ntwv=-1 was not
> set.
> what should I do now? Thans~
> Regards,
> xiaofeng
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Received on Thu May 02 2013 - 02:30:02 PDT
