[gmx-users] Changing cos_acceleration

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 18 19:32:29 CEST 2007

toma0052 wrote:
> Hello,
>      I am working with a DPPC lipid bilayer system in water, and I would like
> to add a shear force to the bilayer.  Preferably, this force would be a
> function of the z coordinate and be maximal at the bilayer surface and decay
> to zero at the box top and bottom.  For this, I have been looking a the
> cos_acceleration option, but it doesn't quite give me what I want.  The
> Manual says that the magnitude of the acceleration is calculated by
> cos(2*pi*z/boxheight).  For the size of the bilayer and box in my system,
> things happen to work out nicely if the magnutude of the acceleration were
> calculated as cos(2*pi*z/boxheight - pi/2).  This would give me an
> acceleration of zero at the box top and bottom as well as the center, and
> maximal acceleration at roughly the bilayer top and bottom surface.  I was
> wondering if there was an easy to make this switch in Gromacs?
>      If there is no easy to do this, I am assuming that I have to modify the
> source code.  I found in update.c a line that reads:
> cosz = cos(fac*x[n][ZZ])
> Would this essentially be the part I am looking for, and I would just have to
> change it to: cosz = cos(fac*x[n][ZZ] - PI/2)?
> Are there other parts of the source code that I would have to change besides
> update.c?
no. your change will work.

> Thank you,
> Mike Tomasini
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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