Greetings,
The first two items developed while working with Tinker 6 output.
boundbox
I am loading Tinker 6 molecular dynamics arc files (which are catenated Tinker
xyz files) that were the result of an NPT dynamics run with periodic boundary
conditions. Subsequently, I read the log file for the run, extract the unit
cell parameters, define boundbox corners for each frame, select the given frame
and:
draw boundbox modelbased mesh nofill
As a drawn object, I expected that I could get different boxes for each frame,
but only the last one is present for all frames. Is there another way to get a
unique box for each frame?
unitcell
When using the unitcell command on the same output, I find that Jmol translates
any atoms that have strayed into an adjacent cell back inside and then draws
bonds that traverse the cell. Is there an override to this recelling process?
Tinker 7 arc files
The Tinker xyz and arc formats have a first line (for each model in an arc
file) that is not actually a header, but gives the number of atoms in the model
with an optional comment following. The latest version of Tinker has added a
second line that lists the unit cell parameters from a periodic boundary
calculation. Jmol throws an error reading this file, with or without a
"Tinker::" identifier (in the case below, when it hits line 12002). I can
provide a complete example if desired. Here are a few lines:
12000 Water Cubic Box (49.323 Angstroms, 4000 AMOEBA)
49.249745 49.249745 49.249745 90.000000 90.000000 90.000000
1 O -2.227074 15.622278 -1.227225 1 2 3
2 H -2.407450 14.671180 -1.453001 2 1
3 H -2.589767 16.087226 -1.993044 2 1
Thanks,
George
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