[gmx-users] Character issues

Justin Lemkul jalemkul at vt.edu
Thu Dec 8 21:00:16 CET 2016

On 12/8/16 2:43 PM, Kelsy Yuan wrote:
> Hi Mark,
> Sorry for the confusion. The command I use is: grompp -p topol.top -f
> engmin.mdp -c 16+mica.gro -zero, I want to do the energy minimization for
> my system that contains 16 stearic acid and a mica surface. I checked all
> my input files as well as the force field files, there is no such line.
> Following is the terminal output:
> -------------------------------------------------------
> Program grompp, VERSION 5.0.6
> Source code file:
> /usr/local/src/gromacs-5.0.6/src/gromacs/utility/cstringutil.c, line: 112
> Fatal error:
> An input file contains a line longer than 4095 characters, while the buffer
> passed to fgets2 has size 4095. The line starts with: '1     AL1     1
>   UNL     A2'      ay1
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------

The input files that grompp reads are whatever you pass to it on the command 
line (.gro, .top, and .mdp) and the force field files.  Since this must be a 
custom force field, there are many potential places for problems, but something 
you created/edited must contain this line.  grompp doesn't do anything it's not 

If you need further help, you'll have to upload all of your files (everything 
listed above) to a file-sharing service and provide a link.

Note that using -zero is potentially dangerous.  If your force field is missing 
interactions and you're just trying to get past them, that may generate an 
unstable system.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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