Hi, Note, that this is indeed the size of the charge groups in the CHARMM force field. You could run pdb2gmx -nochargegrp if you know what you're doing.
Regards, Pär Bjelkmar > I think the notes from grompp are pretty clear. You need to redivide > your charge groups so that they contain fewer atoms. You can do this > in the .top or .itp file and you can find out how to do that in the > manual. Feel free to post your original and charge-group-modified > topologies back here if you want people to take a look at them. > > Chris. > > -- original message -- > > I am trying to equilibrate a POPC membrane with 128 POPC molecules, but > grompp gives out the following notes and minimization with mdrun does not > work. The output on screen of mdrun comes out like this: > Steepest Descents converged to machine precision in 15 steps, > but did not reach the requested Fmax < 10. > Potential Energy = 1.4422483e+17 > Maximum force = inf on atom 4082 > Norm of force = inf > > And grompp notes are: > NOTE 2 [file topol.top, line unknown]: > The largest charge group contains 12 atoms. -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
