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

From: Pratul Agarwal <>
Date: Tue, 12 Feb 2019 13:03:24 +0000


Use the keyword "ntwr", and set it to number of steps after which you want the restart file to be written. The default value is nstlim, this is why you are getting restart file only at the end of the run.

See AMBER manual for details of the keyword.


Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 2/12/2019 5:55 AM, Chetna Tyagi wrote:

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 <><> -o amd2.out -p
PCI.prmtop -c Prod.rst -r amd2.rst -x <><> -ref
Prod.rst -inf <><>*

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,

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Received on Tue Feb 12 2019 - 05:30:02 PST
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