On 6/11/13 9:38 AM, JW Gibbs wrote:
Hi,
As Justin had already suggested, restraints will lead to nasty atomic
clashes. Looking at the gro file you have provided, it seems that the system
is very poorly equilibrated.
I had a similar issue. If the forcefield you are using is accurate enough,
follow the steps as follows:
1. Take the system and increase the box size in all the directions. Run
energy minimization. This will give a somewhat better starting point for the
membrane.
2. Now play around with the box size, such that the x-y dimensions conform
to the reported APL value. Eg., suppose for POPC, you have 48 Lipids per
leaflet and say the experimental APL is about 5.7 nm^2 then the
x=y=sqrt(48*5.7) nm. Adjust the z direction according to what thickness of
water you would want to have.
Doing this assumes that the force field will reproduce experimental APL and,
more often than not, introduces stress on the membrane. The membrane will
probably adjust, but I think this is going to slow equilibration more than anything.
3. Solvate the system (using genbox maybe?). Albeit some water molecules
will penetrate the lipids. Do not worry about that. If your forcefield is
accurate enough, water molecules would diffuse to the top after you follow
steps 4.
Again, this is a barrier to equilibration. I outline one possible solvation
mechanism in my tutorial, and there are water removal scripts on the Gromacs
website. Water diffusion can be very slow and can seriously perturb the lipids.
4. Position restraint the membrane and then use semi-isotropic pressure
coupling but DO NOT position restraint water. Run NPT for maybe 4-5 ns. You
would see that water has diffused to the top and that you have a very good
initial condition.
As I said, it all depends on the correctness of the forcefield that you are
using, but I think any Lipid forcefield will be parameterized such that the
tails would have hydrophobic characteristics and you would not have to worry
about water penetrating the bilayer.
Not always the case, but generally true enough.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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