Steven Neumann wrote:
On Fri, Jan 6, 2012 at 3:48 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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
Thank you Justin. That makes sense. Can you please write me which option
of g_select will do this? How to see the help for each option?
Try:
g_select -select "help all"
Also note that similar procedures to what you want to do are described in the
list archive.
-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
========================================
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