Steven Neumann wrote:
Dear Gmx Users,
I am setting up the simulation of a protein attached to the half of
a nanotube. I set up my system and formed my box and solvated it in
TIP3P water. Water molecules obviously were also placed below the part
of a nanotube where I do not want them to be. Is there any command which
will solvate my system below the surface of the nanotube? Or maybe is
there any command or a software that will allow me to remove those
unwanted water molecules? I have aroun 26000 water molecules in my
system and around 5000 below my nanoutube so with editor it could take
ages. Any suggestions?
You can use g_select to use geometric criteria, i.e. coordinate value > some
number such that only water molecules above a certain point are kept. Then use
trjconv with the index file g_select gives you and you have your cleaned up system.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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/Support/Mailing_Lists/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/Support/Mailing_Lists
