Hello,
this is about cpptraj from AmberTools 1.5.
I was running a simulation containing two molecules. In each of the two
molecules, I selected one atom and initially placed the molecules into
the octahedral box so that those two atoms had a certain distance (about
55 Angstrom).
Throughout the whole MD, I fixed both atoms in their position by
applying harmonic potentials with a large force constant. I used VMD and
its bond label and verified that those two atoms had a distance of about
55 Angstrom to each other throughout the _whole_ simulation.
Then I used cpptraj to automatically extract the distance of those two
atoms from the last frame of the simulation:
distance datasetname .735 .2067 out distancefile
This gave me: 41.5952
I was surprised, because the initial distance was set to about 55 and I,
as described above, also verified that the atoms did not move
significantly during MD. Just out of curiosity, I added the 'noimage'
parameter to the cpptraj command above. This yielded the correct value:
~55 Angstrom.
As stated in the AmberTools 1.5 manual, cpptraj by default applies the
'image' procedure before calculating the distance. In my case, the two
atoms in question definitely did not move out of the primary box,
because they were fixed. Hence, the result should not change with or
without the 'image' procedure.
Is there something wrong with the 'image' procedure in AmberTools 1.5's
cpptraj or do I miss something?
Unfortunately, I did not have the chance to test this with cpptraj from
AmberTools 12 so far.
Thanks,
Jan-Philip
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Received on Fri Jun 22 2012 - 08:30:02 PDT
