[gmx-users] Changing cos_acceleration
David van der Spoel
spoel at xray.bmc.uu.se
Wed Apr 18 19:32:29 CEST 2007
> 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
no. your change will work.
> Thank you,
> Mike Tomasini
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users