[gmx-users] making a artificial layer

David spoel at xray.bmc.uu.se
Mon Feb 9 23:02:01 CET 2004

On Mon, 2004-02-09 at 17:08, Shuaib Shahid wrote:
> hi all;
> i am using gromacs for my fourth year project which involves investigating the electrical double layer.
> i have made a fake atom which i have inserted into a box of water.  My problem is that i have to create a layer of these atoms within a box, which effectively splits the box into two parts of water.  I can then simulate the effect that these atoms have on the water molecules themselves.
> How do i make the solid layer of "fake" atoms??  i think i need to use position restraints but i dont know how.
start with your one atom in a small box (e.g. 0.2 x 0.2 x 0.2 ) alone.
then use genconf to generate a layer:
genconf -f conf -o kkk -nbox 20 20 1
then run editconf to change your box to the required size (and center
your layer)
editconf -f kkk -box 4 4 4 -center 2 2 2 -o lll
then fill it with water:
genbox -cp lll -cs spc216 -o mmm

> thanks
> shuaib shahid
> University of Glasgow 
> Glasgow
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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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