[gmx-users] How can I increase maximum number of pulling step for energy minimization?

[Justin Lemkul]

On 10/28/13 1:59 PM, Gwonchan Yoon wrote:
> Hi gromacs users:
>
> I use gromacs 4.5.6 for energy minimization with steepest descent method
> for ubiquitin pulling simulation with pulling step for applying
> displacement. For that simulation, I should repeat pulling and minimization
> process. I need 10^4 pulling step calculation to get fully unfolded
> structure, but the calculation stops at 503 pulling step with follow error
> message.
>
>
> =====
> Source code file: futil.c, line: 489
>
> File input/output error:
> abc.edr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Sorry!  You were supposed to get help about:
>      mpi-abort
> But I couldn't open the help file:
>      /usr/local/share/openmpi/help-mpi-api.txt: Too many open files.  Sorry!
> --------------------------------------------------------------------------
> =====
>
>
> I open the futil.c line: 489, and that line is as follows.
>
>
> =====
> gmx_file(buf);
> =====
>
>
> However, I cannot catch what should I change to that line.
> If you have any ideas, please let me know.
>

You shouldn't change the source to get around the error.  There's nothing really 
that you can do there.

I/O errors happen when files cannot be read or written to, either because of 
permission problems, full disk, file system glitches, simulation crashing, etc.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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