Hi Justin, Can you tell me where you spotted the broken topology? And where should I get in to get it fixed? Thanks, Ming
On Nov 29, 2017 6:15 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 11/29/17 3:26 PM, MD wrote: > >> Hi, >> >> I was trying to minimize a solvated structure with following commands but >> I >> got stuck at an error message complaining about water molecule not settled >> when I was trying to 'gmx mdrun -v -deffnm em'. I copied the grompp and >> mdrun command, log file and the error message after the command. Any help >> will be appreciated. >> >> 'gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr' >> >> NOTE 1 [file em_real.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 2057414563 >> Generated 97877 of the 97903 non-bonded parameter combinations >> Generating 1-4 interactions: fudge = 1 >> Generated 64492 of the 97903 1-4 parameter combinations >> Excluding 3 bonded neighbours molecule type 'Protein_chain_A' >> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' >> Excluding 3 bonded neighbours molecule type 'Other_chain_B' >> Excluding 3 bonded neighbours molecule type 'Protein_chain_C' >> Excluding 2 bonded neighbours molecule type 'SOL' >> Excluding 1 bonded neighbours molecule type 'NA' >> >> NOTE 2 [file topol.top, line 53]: >> System has non-zero total charge: -0.859995 >> 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. >> >> > You have a fundamentally broken topology. Don't attempt any simulation > with such a topology until you correct it. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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.