[AMBER] Restart file is not formed until the simulation finishes

From: Chetna Tyagi <cheta231.gmail.com>
Date: Tue, 12 Feb 2019 11:55:30 +0100

Dear Amber users,

During accelerated MD simulations, the restart file is not formed until the
simulation has completed (all steps in the input).
So, in my case, the simulation stopped before completing as it ran out of
time at the server.
I can't restart from that point as no restart file is available.

The input file,
  cut=10.0, ntb=1, ntp=0,
  ntpr=1000, ntwx=1000,
  ntt=3, gamma_ln=2.0,
  ethreshd=293, alphad=16,
  ethreshp=-42929, alphap=2311,

And my command,

*mpirun pmemd.cuda.MPI -O -i amd.in <http://amd.in> -o amd2.out -p
PCI.prmtop -c Prod.rst -r amd2.rst -x amd2.nc <http://amd2.nc> -ref
Prod.rst -inf amd2.info <http://amd2.info>*

What am I missing? And how can I solve this problem?

I have not found any way to restart using the trajectory (.mdcrd or .nc
file) but is there any way?

Thank you,

Best wishes
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Received on Tue Feb 12 2019 - 03:30:02 PST
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