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

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 5 22:33:24 CET 2001

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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