Re: [AMBER] Nonbond cells Problem How to restart?

From: Daniel Roe <>
Date: Fri, 8 Nov 2013 07:54:22 -0700


On Fri, Nov 8, 2013 at 12:27 AM, Soumendranath Bhakat
<> wrote:
> *Please let me know *
> *1. How to restart now. I have the output files equil.out;equil.rst. How to
> restart it from step 13500. I don't want to overwrite it. I want to write
> the the remaining steps from 13500 till the last in the equil.out file
> only.*

Just use the restart file as your input coordinates for a new run with
irest=1 and ntx=5; make sure you specify new files names for all of
your output files. Unfortunately since you are using the Langevin
thermostat you will not be able to exactly recover your trajectory
from 13500 onward; this is because the random number stream will be
different. However, this won't affect the fidelity of your simulation

> *Note: We use this command for submission of equil job " time mpirun -np 10
> pmemd.cuda -O -i <> -o equil.out -p
> -c Heating.rst -r equil.rst -x equil.mdcrd & "*

Don't use mpirun with pmemd.cuda! What you are doing here is launching
10 competing copies of pmemd.cuda, which at best will unnecessarily
tax your system, and at worst will result in file corruption due to
separate threads trying to write to the same file at the same time.
Just run pmemd.cuda by itself. If you have multiple GPUs you can use
pmemd.cuda.MPI or use pmemd.cuda in combination with setting
CUDA_VISIBLE_DEVICES; see many earlier posts on the list for more


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Nov 08 2013 - 07:00:05 PST
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