[gmx-users] MD problem with nwall=2

[Peter C. Lai]

On 2012-09-06 02:46:21PM +0200, Bogdan Costescu wrote:
> On Wed, Sep 5, 2012 at 8:37 PM, Peter C. Lai <pcl at uab.edu> wrote:
> > Could be a result of not setting x/y compressibility = 0 as the manual
> > suggests you should do...
> 
> As one who has also tried to use walls recently, I've also found this
> statement in the manual, but no further explanation. Anyone cares to
> expand on it ?
> 
> For testing, I've recently performed a run with compressibility=0 for
> z and non-zero for x/y (so, exactly opposite to what the manual
> suggests :)). The box deformed as expected in x/y and the pressure
> seemed to be maintained correctly. Is there some reason for which this
> would be a random (i.e. not easily reproducible) result ? Or are there
> some less obvious problems with it ?

I am trying to use walls with lipid bilayers. I once also applied a non-zero
compressibility to x/y , and my bilayer physically collapsed in less than 1ns,
although the simulation appeared to be otherwise nominal.

Another thing I noticed was that the value of wall_density is important, 
since a small leakage past the wall may not be noticeable until you exceed 
1-10ns and that will quickly drop volume to 0 and make it look like x/y has 
collapsed (and cause a system crash due to exceeding pme/dd tolerances).

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