Ok, thank you Justin. Ming On Nov 29, 2017 6:55 PM, "Justin Lemkul" <jalem...@vt.edu> wrote:
> > > On 11/29/17 6:53 PM, MD wrote: > >> Hi Justin, >> Can you tell me where you spotted the broken topology? And where should I >> get in to get it fixed? >> > > "System has non-zero total charge: -0.859995" > > Can any molecule have a fraction of an electron? > > Whatever you've manually parametrized is incorrect. > > -Justin > > 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. >>> >>> > -- > ================================================== > > 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.