[gmx-users] input/output error in production grompp

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 13 13:52:06 CEST 2012

On 6/13/12 7:36 AM, Malai wrote:
> Hi,
> I used the command following to generate .tpr file for production but I got the
> following error. Without considering this error, I run production but it is
> working now. any problem will be in production?

The command below makes no sense; how is it that you were able to produce a .tpr 
file for your simulation?

> -v -f hex1.mpb -c hex1.pdb -p hex1.top -o hex1.pdb

This is not the command you typed (it contains several errors, both logical and 
typographical), and it certainly has nothing to do with the error below, as no 
reference is made to a file called "hex1.gro."  When reporting problems, please 
always copy and paste directly from your terminal.  Re-typing what you think you 
typed is error prone and wastes time.

> Error:
> Program grompp, VERSION 4.5.4
> Source code file: futil.c, line: 491
> File input/output error:
> hex1.gro
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors

I/O errors occur when either a file isn't found in the working directory (i.e. 
doesn't exist) or can't be produced (insufficient permission or disk space to 
write the file).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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