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:
++++++++++ 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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