In addition to what Joao said, the fixed-width .pdb format is fundamentally unsuited to large systems. You need to find a way to avoid using such a .pdb file as input to pdb2gmx; either solvate later, or use a different format for input.
Mark On Mon, Aug 4, 2014 at 11:09 PM, WH <signoreguid...@163.com> wrote: > Dear Gromacs users, > > I want to use Gromacs to process a system with more than 80000 water > moelcules. However, when use pdb2gmx to deal the the pdb file, the out put > .gro file has the form like this: > 3409HOH HW234995 -5.617 -6.883 -8.771 > 3409HOH OW34996 -6.108 -6.959 -7.760 > 3409HOH HW134997 -6.107 -6.973 -7.855 > 3409HOH HW234998 -6.199 -6.971 -7.735 > 3409HOH OW34999 -4.964 -8.455 -9.110 > 3409HOH HW135000 -5.054 -8.441 -9.081 > 3409HOH HW235001 -4.939 -8.372 -9.150 > 3409HOH OW35002 -6.157 -7.576 -8.913 > 3409HOH HW135003 -6.187 -7.499 -8.962 > > Only 4 digits will be used for the residue number and 5 for the atom > number. Thus, the actual residue number and atom number cannot be written > correctly and lead to failure for the MD simulation. > Does anyone know how to fix this problem? I really appreciate it. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.