[Chimera-users] alter to periodic box

paul buscemi pbuscemi at q.com
Sat Jun 17 11:44:53 PDT 2017

I was experimenting with mixed solvents and found that if you create a box around a molecule say 10A on a side,  then de-select "remove solvent" and then create a second box, say 2A on a side,  that second box forms around the first.  You can then constrain the second box which will for the most part retain the first and the parent molecule during a simulation.  This allows visualization of the live trajectory as well.  I used MON around water and he process is faster to create than selecting the six outside surfaces of a solvent box.


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