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? BUt I don't understand how just like that we creat an empty place and water move to this place??
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://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
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