[gmx-users] genconf, grompp

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 10 03:31:02 CET 2012

saly jackson wrote:
> Hi everybody
> After using genconf to build a .gro file for example containing 100000 
> molecules, I want to use grompp to minimize the system as the following:
>   genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro
> grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1

You should not invoke the -maxwarn option unless you completely understand the 
implications of the error(s) you are bypassing.

> Although I see in the H-largebox.gro file 100000 molecules coordination,
> I receive the following error after running grompp.
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: grompp.c, line: 1370
> Fatal error:
> There was 1 error in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> "Just a Minute While I Reinvent Myself" (Red Hot Chili Peppers)
> Would you please help me?

There is no way to help you.  The actual error message is further up in the 
grompp output, which you have not included.



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


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