[gmx-users] non squares box

David van der Spoel spoel at xray.bmc.uu.se
Sun Jun 21 14:57:48 CEST 2009

Omer Markovitch wrote:
> I prefer to keep discussions professional, Mark and Tsjerk.
> Anyway, I am doing MD with PBC. I have a surface which sits on the XY 
> axes, the surface is not a square and my question is how do I tell 
> gromacs that I have a non standard box. Please see my original post for 
> more details:

Dear Omer,

I agree with Tsjerk that genconf is a useful tool to visualize the 
periodicity using PyMol, as was suggested. If you dismiss this kind of 
advice and repeat the original question, people get upset.

What you are saying is that you generated a box using editconf, but 
editconf does not put the atoms in the box. Hence putting a box that 
does not correspond to the coordinates will give rise to atomic clashes.

I'm not quite sure what you think should be the expected result of your 
trjconv operation.

> ++++++++++
> I would like to ask your help on the following - I want my simulation to 
> include a surface, and have PBC.
> The surface I chose is aligned on the XY plane. However, the surface is 
> not a square.
> The surface dimensions are a=b=169.2 & c=6.9 Angstroms, the angles are: 
> bc=ac=90 & ab=120 degrees.
> I have used "editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0". 
> To test this, I have used "trjconv -pbc nojump -center yes -boxcenter 
> zero". My problem is that the trjconv generates a structure where some 
> of the surface atoms are cut and/or overlapping...
> ++++++++++
> Thank you. Omer.
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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David van der Spoel, PhD, Professor of Biology
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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