Smiruthi Ramasubramanian wrote:
I am simulating an ion channel and require help placing a concentration
of ions at one side of the box (below the membrane).
"Sidedness" is irrelevant in a periodic system; the water layers are continuous
with PBC.
SETUP: membrane + embedded protein in the center of the cube.
I tried to generate a smaller cube (of the required volume below the
cube), solvate, add ions and then /cat/ with the *.gro file of my system
before solvating. But when I solvate the system with ions, the ions are
removed.
Any suggestions as to how to handle this problem?
I don't fully understand what you tried to do, but it should be possible to
solvate the unit cell normally, create an index group for the waters on one
"side" of the membrane, and pass this index file to the -n flag of genion.
Creating the index file may involve writing your own script to collect the atom
numbers. As far as I am aware, make_ndx cannot, for example, select all water
molecules below/above some z-coordinate, which would be required for your situation.
-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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