[gmx-users] MD problem with nwall=2

Peter C. Lai pcl at uab.edu
Fri Sep 7 21:38:50 CEST 2012

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).

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|

More information about the gromacs.org_gmx-users mailing list