[gmx-users] Pressure coupling type for Biomembrane simulation
yhsong at ccb.wustl.edu
Wed Dec 31 18:40:01 CET 2003
Thanks David. For the 6 pressure scaling values needed for xx, yy, zz,
xy/yx, xz/zx and yz/zy, if xy/yx, xz/zx and yz/zy are set as 0.0, xx, yy, zz
are set as the same number, Does it has differenec from the iostropic
pressure coupling way? Also, for the compressibility, the typical value is:
4.5e-5 (mostly used that I see in the tutorial etc), are there some reasons
for choosing the compressibility in xx, yy, zz as 4e-5 other than 4.5e-5?
> >I am doing the biomembrane simulaiton, I am wondering that now the
> >in the Biomembrane simulations deal with the pressure coupling type for
> >Biomembrane simulation. Using pcoupltype as isotropic or anisotropic,
> >one is more physiological reasonable? Also if choosing the anisotropic,
> >should be the 6 pressure scaling values needed for xx, yy, zz, xy/yx,
> >and yz/zy components respectively.
> no expeert, but anisotropic
> compress = 4e-5 4e-5 4e-5 0 0 0
> the last values prevent your box from becoming skewed.
> >Thank you very much in advance.
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> David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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