On 6/21/17 10:45 AM, Sergio Manzetti wrote:
Hi Justin, the sequence was: gmx editconf .... gmx solvate .... gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA -nname CL then: gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o dna_solv_NaCl_EM gmx mdrun This worked. Then for the sim: dna_solv_NaCl_EM.gro does not contain any ions.
You didn't pass topol_solvated.top to genion -p, so it did not update the number of ions. Your final call to grompp should have triggered an error because the contents of the system will not match, unless you did this manually. But again, it is *impossible* for mdrun to delete anything. So check the contents of your files carefully, even just in a text editor for coordinates and topology, to make sure you have what you think you have.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
