[gmx-users] Adding ions using "genion"

[cuong nguyen]

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.

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 GROMACS
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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