[gmx-users] Adding ions using genion
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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Adding ions using genion
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 listgmx-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
Re: [gmx-users] Adding ions using genion
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. Mark 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 listgmx-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
