Thank you so much. You mean first use gmx solvate, then delete the Sol molecules which i dont need them? So trjorder can fix the rest, yes?
On Mon, 16 Apr 2018, 16:26 Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 4/16/18 5:58 AM, rose rahmani wrote: > > Hi, > > > > I have input structure from my last simulation. The box is 12nm long in Z > > axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 > to > > 12 is empty) . I want to add solvent between z=3-8. How can i do that? > > The problem is that i cant adjust wall and sheet( z coordination) to > start > > from z=0 of box. > > I mean when i extract wall and sheet from my last simulation and open it > in > > a viewer they wont start from 0, which is not odd. So i cant use the box > > size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box > > larger. > > What is your idea? Is there any tool to add solvate in specific > dimensions? > > No. > > > Would you please help me? > > Write a script to remove solvent molecules based on coordinates, or use > gmx select write an index group to do the same. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
