[gmx-users] Slow-Growth Pressure/System Volume Anomaly

David L. Bostick dbostick at physics.unc.edu
Thu Dec 6 00:33:40 CET 2001

Hello David,

I have viewed the .gro file output by mdrun 200 ps after the perturbation.
This is before the system goes back to normal pressure and volume.  The z
dimension of the box is larger than the system.. i.e. the water above and
below the bilayer hasn't moved to catch up with the z-dimension of the box.
So, in this sense, yes there is a vacuum, but the system stays together
long enough for the box to snap back into shape (about 500 ps).


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

On Wed, 5 Dec 2001, David van der Spoel wrote:

> On Wed, 5 Dec 2001, David L. Bostick wrote:
> >During the run using slow growth, I used anisotropic coupling of pressure
> >(also used in the equilibration).  However, I observe a huge spike in the
> >system pressure (~0 kJ/mol/nm^3 -> ~4000 kj/mol/nm^3) and
> >volume (~570nm^3 -> ~770nm^3).  I also see a huge rise in the Total Energy
> >(-5e-5 -> -1.5e-5).  
> >
> >After this perturbation, I imposed the original forcefield again and
> >eventually, the system pressure, volume, and energy went back to "normal." 
> >I would like someone's opinion on this before I attempt to assign any
> >physical meaning to this.  Is anything in mdrun turned off when using
> >slow-growth FEP?  Can anyone think of any reason for this to occur?
> Isn't some kind of phase change in the lipids, i.e. collective
> conformational change? Have you looked at the animation of the trajectory?
> Do you get vacuum bubbles in the box?
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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