Hi Yun, Well, within 2 nm periodic images can influence each other through ordering of water. But how much that will affect your results and how relevant it is for the properties you're after is hard to tell. I think most people will just continue with analysis, saying that there have been no direct interactions.
Cheers, Tsjerk On Nov 10, 2011 6:42 PM, "Yun Shi" <yunsh...@gmail.com> wrote: Hi Tsjerk, Thanks for the advice. After I did the nojump conversion of trajectories, there were still quite a few frames with min. dist. under 2.0 nm, but all of them were above 1.4 nm, which I set for rvdw. This is not "ideal", but I wonder if it's still OK to use this trajectory? Thanks, Yun Message-ID: <cabze1sg24mu7zsh7asvmfainrjsmvgkomg3uy-ixftokwvr...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi Yun, Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before using g_mindis... -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20111110/7b9ed4a5/attachment-0001.html ------------------------------ -- 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
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