[gmx-users] External Force and Box Size

[David van der Spoel]

On 3/9/10 9:43 AM, Archana S Achalere wrote:
>
> Hi all,
>
> I am simulating lipid + water system. I am appling external force on
> both the species in the system.
>
> After few 100 thousands of time steps the simulation gets terminated and
> it gives me an error message:
> "The Z-size of the box (2.000094) times the triclinic skew factor
> (1.000000) is smaller than the number of DD cells (2) times the smallest
> allowed cell size (1.000000)"
>
> Can anyone please help me in resolving this error.
>
> I am using the following options:
>
> coulombtype = PME
> vdw-type = Cut-off
> Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p = 1.0 1.0
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
>
> Thank you.
>
> -archana.
>
Your box is becoming long and thin. Are you sure it makes sense to apply 
an external force while simultaneously doing pressure coupling? Maybe 
you should turn off the pressure coupling in the plane of the membrane, 
or make it isotropic. Anisotropic can lead to this, since the membrane 
needs to be intact to maintain the surface tension necessary to keep the 
box shape. If you use anisotropic coupling an a box without appreciable 
surface tension, e.g. decane/water this same effect will happen: the 
surfare area is minimized indefinitely.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se