Thanks a lot for your answer. So by increasing the z coordinate after solvated the system we induce creation of a empty space above the solvated box. After minimisation a few water molecules move above its new empty space because their link are not strong enough.
2013/5/13 Justin Lemkul <jalem...@vt.edu> > > > On 5/13/13 8:01 AM, Nawel Mele wrote: > >> So we just compute an interface vacuum-water like the picture in attach in >> increase the coordinate value of the z-axis of the box? >> > > The list does not accept attachments. If you want to post an image or > file, provide a public link to access it. > > > BUt I don't understand how just like that we creat an empty place and >> water >> move to this place?? >> >> > Seems like intuitive behavior to me. Think about basic physics and > thermodynamics. > > -Justin > > >> >> 2013/5/13 Justin Lemkul <jalem...@vt.edu> >> >> >>> >>> On 5/13/13 6:10 AM, Nawel Mele wrote: >>> >>> Hi all, >>>> >>>> I am performing a simulation of protein at air/water interface. >>>> >>>> For create an air-water interface I just expand the box in the z >>>> direction. >>>> So,aAfter minimization we can noticed that water molecules moved out of >>>> bulk water in the z direction. >>>> >>>> Why you just need to expand the z-axis for obtain this interface?? I >>>> don't >>>> understand the mechanism. >>>> >>>> >>>> You're not creating an air-water interface by doing this, you're >>> creating >>> an vacuum-water interface and your water molecules are evaporating into >>> the >>> empty space. >>> >>> -Justin >>> >>> -- >>> ==============================****========== >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================****========== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<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<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >> >> >> >> >> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- *Mlle* Mele Nawel Master 2 In Silico Drug Design University of Paris Diderot/Strasbourg -- 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
