[AMBER] Nonbond cells Problem How to restart?

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Fri, 8 Nov 2013 09:27:23 +0200

Hii all;

We are running equil step in amber GPU. the equil in file is looking like
Equilibration Step of MMP3 (MMMM): stage-1
  imin= 0,
" After finishing the job till step 13500 it shows an error " Nonbond cells
need to be recalculated, restart simulation from previous checkpoint with a
higher value for skinnb." As suggested previously not to worry about the
skinnb and restart it from previous good restart file (
http://archive.ambermd.org/201306/0376.html). Now I have the equil.rst file.

*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

*Please let us know how to restart it now.*

Your help will be highly appreciated.

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

Thanks & Regards;
Soumendranath Bhakat
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Received on Thu Nov 07 2013 - 23:30:02 PST
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