On Thu, Nov 24, 2011 at 5:16 PM, cuong nguyen <nvcuon...@gmail.com> 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)
There is a mis-match between your .top file and .gro file. > (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 > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists