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

Justin Lemkul jalemkul at vt.edu
Tue Jun 11 15:48:17 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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