[gmx-users] Adding ions using "genion"

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 24 10:39:52 CET 2011

On 24/11/2011 8:16 PM, cuong nguyen wrote:
> Dear,
> I create a box of water with 10 MIBC molecules on two opposite surfaces.
> then I used the command "grompp -f input_min.mdp -o min.tpr -c 
> box1.g96" to creat .tpr file before using the command "genion -s 
> min.tpr -o add.gro -nname Cl -pname NA -nn 20 -np 20" to add 20 Na+ 
> and 20 Cl- into this box.
> I run the command "grompp -f input_min.mdp -o min.tpr -c add.gro" 
> again and appeared the warings :
> Warning: atom name 176 in topol.top and add.gro does not match (CL - OW)
> Warning: atom name 177 in topol.top and add.gro does not match (CL - HW1)
> Warning: atom name 178 in topol.top and add.gro does not match (CL - HW2)
> Warning: atom name 179 in topol.top and add.gro does not match (CL - OW)
> Warning: atom name 180 in topol.top and add.gro does not match (CL - HW1)
> (more than 20 non-matching atom names)
> WARNING 1 [file topol.top, line 72]:
>   21754 non-matching atom names
>   atom names from topol.top will be used
>   atom names from add.gro will be ignored
> ......
> Fatal error:
> Too many warnings (2), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> then I tried with the command "grompp -f input_min.mdp -o min.tpr -c 
> add.gro -maxwarn 2000" and it run well.

No, it ran poorly, because you didn't understand what you were doing 
with -maxwarn. Your atom ordering must match between the .top and .gro 
files. Ignoring the warning doesn't fix the problem.


> However, when I kept working with the command "mdrun -s min -o min -c 
> min.g96 -x min -e min -g min", the errors appeared as follow:
> Fatal error:
> 3 particles communicated to PME node 2 are more than 2/3 times the 
> cut-off out of the domain decomposition cell of their charge group in 
> dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the 
> website at http://www.gromacs.org/Documentation/Errors
> Please help me to fix this problem.
> Many thanks.
> Nguyen Van Cuong
> PhD student - Curtin University of Technology
> Mobile: (+61) 452213981

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