Hi All, I am running a membrane protein MD simulation with Gromacs 5.1.4. I want to add some substrate molecules(acetate) to my system, and I used this command: "gmx insert_molecules -f ###.pdb(include the ptotein, POPC, etc.) -ci act.pdb -o ###.pdb -nmol 48 -box 6.7 6.7 8.1 -try 500 -rot xyz", but then I found many acetate molecules are put out of the system in the out .pdb. Is that normol or wouldl affect the later MD process? If so, how can I fix it. Any suggestions would be greatly appreciated. Thank you in advance!
All the best, Wu Meng -- 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.
