[gmx-users] [Fwd: janusik at mp.wsp.czest.pl]

David van der Spoel spoel at xray.bmc.uu.se
Mon Jun 30 16:55:01 CEST 2003

>I am new user of this one and I have a problem. Could you help me. please?
>I have build polymer structure in Gromacs program with periodic boundary
>condition but I would like to build thin film with thicknes 1 nm. I have
>aplied evald_geometry. My cell is cubic with parameters 2.5 nm. Can I
>apple -scale obtion to decrease z dimension -scale 1 1 0.4. It will be
>anough to have thin film in vaccum?

>Could you help me?

If you just scale you will get huge forces. It would be better to perform an MD run 
with anisotropic pressure scaling, i.e. you allow the box to fluctuate
in size. Then you apply a pressure of 1000 bar in the Z direction and
1 bar in the x and y directions. You might need semiisotropic scaling for this.

Serwery www od 7 zl m-c
Projektowanie stron od 200 zl
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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