Dear all, I have a system of POPC/Protein/water/ions to simulate. I am trying to simulate this system by getting ideas from Justin's tutorial of kalp15-dppc. I've passed all steps of EM, NVT, and NPT as I expected. But when I want to run mdrun, I get some errors about waters can not be settle. So, I tried to remove them from npt.gro, update the number of atoms in .gro file, and then update number of SOL molecules in top file.Finally I made a new index file to go on.
Next, to start mdrun, I run this command: grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index-new.ndx -o md_0_1.tpr and get this fatal error: Number of atoms in Topology is not the same as in Trajectory. In fact, I thought of updating npt.cpt file, but it's a binary file and I guess it's impossible. Does anybody knows what should I do? Would you please give me advice? Thanks in advance. Sincerely, Shima -- 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
