On 03.06.2013 18:43, Neha wrote:
I am a new user to Gromacs and am working on lipid simulations with the
Martini forcefield. The Martini website provides a pre-equilibrated DPPC
bilayer, and I was wondering if there were any told that would allow me to
convert this bilayer into a monolayer. For periodic boundary conditions to
work, I was thinking of a stack that would go like
Water
Lipid Heads
Tails
Vacuum
Tails
Lipid Heads
Water
Is this the 128 DPPC system from
http://md.chem.rug.nl/cgmartini/index.php/downloads/example-applications/66-dppc-membrane
(2x 64 DPPC + 2000 W)?
Is there any way to split apart the provided bilayer using some combination
of Gromacs tools and introduce a space of at least 10 nm which is apparently
the distance needed for the tails to not interact with each other?
The layers are, 'afaics', somehow interdigitated and placed in a box
normal to z with a z height of 10nm and centered at about 5nm. They
are not sorted (first 64 lower, secod 64 upper layer).
If there is no way of simply splitting the bilayer, what would you recommend
for creating a simulation of lipid monolayers from a single DPPC molecule? I
feel like I could use genconf but it might require too much equilibration. I
am hopeful that there is some way of simply working with the provided
bilayer.
What I would do: write a simple script, read 12 lines (one molecule) and
check for the z coordinate of the NC3 type (first entry of each 12 line
record). Then, decide:
- if NC3[z] > 6 then add 1.0 to all 12 z coordinates (nm)
- if NC3[z] < 4 then keep it
write the 12 lines back to another file, either modified or unmodified.
next 12 lines/molecule (128 times total)
Then, the waters. This is somehow arbitrary. Maybe you could check if
each water's (W) z coordinate is below 5, so keep it - or above 5,
so move it up. This will, of course, require some steepest descent
minimization afterwards.
--
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