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EoF during reading of restart file
#38045 08/17/20 09:41 AM
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cm14sjm Offline OP
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Hi

I've been running several simulations for different trajectories all of which require restarting after a 48hr job timeout on the HPC. I have 20 trajectories running all of which ran for the full time, but only one of these has a restart file with anything in it. All the trajectories use the same input file (attached). Is there any reason why only one trajectory should have a restart file with any content or any way to solve this?

Thank you in advance

Attached Files
1tit_02_001_inp.txt (4.35 KB, 20 downloads)
SHA1: 1b7152af39fd169439c84fbf87b552a9fc676610
Re: EoF during reading of restart file
cm14sjm #38046 08/17/20 02:13 PM
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rmv Offline
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The restart files are not written unless the simulation completes; an interruption via timeout would not write a restart file.

How large is your system? The DIMENSION command may be wasting large amounts of memory, which could make your job run more slowly.


Rick Venable
computational chemist

Re: EoF during reading of restart file
cm14sjm #38050 08/18/20 08:35 AM
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cm14sjm Offline OP
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There's about 700 atoms in the protein and 30000 atoms in the solvent, so if I reduced DIMENS to 31000 should that make it run faster and complete the restart file?

I also added 'ISVFRQ 1000' to dynamics section of the input to try get around this, should I delete this?

Thank you for all your help

Re: EoF during reading of restart file
cm14sjm #38051 08/18/20 08:38 AM
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Change NSTEP so that the job finishes within the allowed time. This is the best way. Changing DIMENS will not have a great effect on the performance (if any at all), and it is cumbersome to stitch together tracectory pieces.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: EoF during reading of restart file
lennart #38052 08/18/20 08:50 AM
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cm14sjm Offline OP
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Thank you, I"ll change nstep. Is it worth me deleting ISVFRQ 1000 too? Thanks

Re: EoF during reading of restart file
cm14sjm #38054 08/18/20 02:53 PM
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rmv Offline
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You can simply remove DIMENS command for systems with less than ca. 300,000 atoms

Do not use ISVFRQ


Rick Venable
computational chemist


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