<div dir="ltr">I prefer to keep discussions professional, Mark and Tsjerk.<br><br>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:<br>
<br>++++++++++<br>I would like to ask your help on the following - I want my simulation to include a surface, and have PBC.<br>The surface I chose is aligned on the XY plane. However, the surface is not a square.<br>
The surface dimensions are a=b=169.2 & c=6.9 Angstroms, the angles are: bc=ac=90 & ab=120 degrees.<br><br>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...<br>++++++++++<br><br>Thank you. Omer.<br clear="all"> <br>Koby Levy research group,<br>Weizmann Institute of Science. <br><a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br>
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