I don't think the atom number is the problem. I also have systems with more than 99999 atoms, and in the gro file the atom number after 99999 is reset to 0, but that was never a problem for the simulations. I would check the parameters again, but I don't have a more exact answer to your problem.
2010/3/5 Carla Jamous <carlajam...@gmail.com> > Hi, > please I'm having a problem while running a minimisation. > > I prepared my system with pdb2gmx and generated .pdb files. From the last > pdb file, I did grompp & generated the tpr file that I used to start my > minimization. At the 46th step, I encountered the problem:"water molecule > cannot be settled". > I looked at the pdb file and found that many water residues have the same > number because above residue 9999, it restarts to count residue 0, 1, etc... > > I prepared the same system but I generated .gro files instead of .pdb & > started my minimization. But did't encounter the same problem. > I looked at the gro file & here, it's the atomic number that can't be above > 99999. > > So did anyone encounter this problem before, & if yes, please do you have a > solution to propose? > > Thanks > > Carla > > > -- > 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/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/mailing_lists/users.php >
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