Hi,<br>
<br><div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">> 2. editconf -f CORE_MTB.gro -o CORE_MTB.gro -d 0.8<br>><br>> WARNING: No boxtype specified - distance condition applied in each dimension.
<br>> If the molecule rotates the actual distance will be smaller. You might want<br>> to use a cubic box instead, or why not try a dodecahedron today?<br><br>Unless you can say why you want a triclinic box (the default), while
<br>you're learning I strongly recommend a cubic box... use the -b option<br>appropriately.<br><br></blockquote></div><br>
Actually, it would be good to get yourself used to the rhombic
dodecahedron as a default (-bt dodecahedron). It's relatively small and
you'll avoid 'box corner effects'. So, especially for beginners,
there's no box like a rhombic dodecahedron box.<br clear="all"><br>
Cheers,<br>
<br>
Tsjerk<br>
<br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands
<br>+31 50 363 4336<br>