[gmx-users] Re: restraints on water oxygen atoms

JW Gibbs hanniballecter13 at gmail.com
Tue Jun 11 15:38:15 CEST 2013


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

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. 

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. 

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. 

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