Re: [AMBER] simulation stop due to size limit exceed

From: Chris Neale <candrewn.gmail.com>
Date: Thu, 21 Sep 2017 10:16:05 -0600

The error message indicates that you don't have any space left on disk (or
within your quota). You'll have to solve that problem before you worry
about how to do a restart, though see below:

in=A
out=B
pmemd -i md_restart.in -o ${out}.out -p this.prmtop -c ${in}.rst -r
${out}.rst -x ${out}.mdcrd -inf ${out}.info -l ${out}.log

and:

$ diff md.in md_restart.in
5,6c5,6
< irest=0, ! ires=1 for restart and irest=0 for new start
< ntx=1, ! ntx=5 to use velocities from inpcrd and ntx=1 to not
use them

---
>     irest=1,       ! ires=1 for restart and irest=0 for new start
>     ntx=5,         ! ntx=5 to use velocities from inpcrd and ntx=1 to not
use them
On Thu, Sep 21, 2017 at 6:36 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> I ran the simulation for 25000000 steps every time it stops at  756500
> steps. How I can manage or use restart the simulation from the step where
> it stop in the previous run.
>
> /var/spool/torque/mom_priv/jobs/15065197.amino-alpha.arc-ts.umich.edu.SC:
> line 7:  5107 File size limit exceeded/nfs/amino-library/local/Amber$
>
>
> Regards
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>
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Received on Thu Sep 21 2017 - 09:30:03 PDT