Hi Justin, Thanks for your answer, On Thu, Aug 13, 2009 at 11:42 AM, Justin A. Lemkul <[email protected]> wrote:
> > > Jamie Seyed wrote: > >> Dear all, >> I want to know how can I use genbox to fill inside of the pore as well as >> a layer outside. From the "man genbox" page I try to use -shell with a >> negative value (?) but it put waters far from the outside of the pore and I >> think it does not care about the sign. It seems strange to me because when I >> had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I got a >> layer of few molecule around the pore, but when I change it to 1. 1. 1., the >> water molecules generated far away. I appreciate if someone tell me (1) how >> I can add water inside the pore and (2) why >> > > (1) The -vdwd option may help, or even -ci -nmol. If you have a pore, > wouldn't water diffuse in over time anyway during equilibration (assuming an > otherwise correct setup and realistic physical model)? Long time ago I did an experiment on water in confined geometry and I want to see if the results can obtain from the simulation... So for using -nmol -ci (at random position), it says I must use a file like insert.gro would you please explain me how I can make insert.gro? > > (2) If you haven't re-positioned your system within the box, it probably > doesn't make any sense. The Gromacs convention is to place the corner of > the box at the coordinate origin, and everything else is relative to that. > Is a 1-nm cubic box large enough to encompass your system? If not, genbox > is doing what it's told - filling a 1-nm box near the origin, and leaving > everything else out. > > -Justin > > changing the box size will give a opposite result. Please advise..Thanks >> in advance/Jamie >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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