The text of the error has nothing to do with the ions you may or may not need to add. Please read more closely.
Mark On Wed, 1 Jun 2016 06:57 kamakshi sikka <kamakshi.si...@gmail.com> wrote: > Hello, > > I am doing mixed lipid bilayer simulation with a peptide. This bilayer > membranewas built by Charmm Gui. Afterwards, I oriented the peptide on the > top of the bilayer and then saved the peptide+membrane complex file. Then , > I am trying to add ions into the system by giving the command mentioned > below.But, this is giving an error. This membrane already has 'SOD' > ions in it. Is it creating a problem while adding CL ions into the system? > Please help. > > *COMMAND:* > gmx grompp -f ions.mdp -c complex_new.pdb -p topol.top -o ions.tpr > > > NOTE 1 [file ions.mdp, line 17]: > ions.mdp did not specify a value for the .mdp option "cutoff-scheme". > Probably it was first intended for use with GROMACS before 4.6. In 4.6, > the Verlet scheme was introduced, but the group scheme was still the > default. The default is now the Verlet scheme, so you will observe > different behaviour. > > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# > > NOTE 2 [file ions.mdp]: > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > that with the Verlet scheme, nstlist has no effect on the accuracy of > your simulation. > > Setting the LD random seed to 2538245621 > Generated 73900 of the 73920 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 47534 of the 73920 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein_chain_A' > Excluding 3 bonded neighbours molecule type 'POPS' > Excluding 3 bonded neighbours molecule type 'POPC' > Excluding 2 bonded neighbours molecule type 'SOL' > Excluding 1 bonded neighbours molecule type 'SOD' > > NOTE 3 [file topol.top, line 2253]: > System has non-zero total charge: 5.000001 > Total charge should normally be an integer. See > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > for discussion on how close it should be to an integer. > > > > > ERROR 1 [file topol.top, line 2253]: > ERROR: The cut-off length is longer than half the shortest box vector or > longer than the smallest box diagonal element. Increase the box size or > decrease rlist. > > > Removing all charge groups because cutoff-scheme=Verlet > > There were 3 notes > > ------------------------------------------------------- > Program gmx, VERSION 5.0.2 > Source code file: > /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/grompp.c, line: 1723 > > Fatal error: > There was 1 error in input file(s) > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > Regards > Kamakshi Sikka > -- > 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.