I did hope the ions will move out eventually. But after my ~70ns of conventional MD (with duplicate MD runs and the protein as a dimer with identical sequence), they were still there in the binding site.
So I assume it would be much better to start without any salt ions beside my ligand. Could anyone suggest a way around this? Thanks, Yun On Mon, Nov 26, 2012 at 12:39 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 2012-11-26 21:28, Yun Shi wrote: >> >> Hi everyone, >> >> I am doing conventional MD of a protein-ligand system with a mobile >> loop as part of the binding site. >> >> Presumably, the positive Arg side chain on the mobile loop will >> eventually move towards the negative carboxylic group on my ligand. >> But I found the addition of NaCl (0.15 M conc.) had some effect on >> this movement, since the random addition could put Na+ or Cl- ions >> between the mobile loop and my ligand. >> >> I tried generating a index containing only SOL far not close to my >> ligand, but apparently genion requires a continuous solvent group. So >> is there any other way to achieve this? Trying different numbers for >> -seed option seems inefficient and is dependent on luck. >> >> Thanks, >> Yun >> > Maybe your assumption is wrong? > > Run a long MD simulation and you will find out. > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists