On 11/29/17 5:02 PM, MD wrote:
Hi gromacs folks, I was trying to do a mdrun using nvt.mdp and I got following error messages. I am not quite sure what is causing the error and I am hoping to get some help here. Is it because my starting structure is not good enough? There were some broken residues but I had them fixed and the minimization run was ok until the equilibration. The command and notes I had was as followed. * gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr* Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12# Setting the LD random seed to 552293178 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' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Other_chain_B' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_C' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... NOTE 1 [file topol.top, line 53]: System has non-zero total charge: 0.140005 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.
This is the same error as your previous question. Don't ignore grompp when it's trying to help you avoid really bad mistakes.
-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.
