periodicity not handled correctly in trjconv when converting to pdb
I'm having problems generating a pdb file in 3.3 that handles periodicity
correctly. In particular, I've tried trjconv on my trajectory to generate a
multi-frame pdb file. g_dist indicates that the ligand remains at a stable
distance from some refernece atoms in the protein throughout the entire
trajectory (as does ngmx), but none of the different pbc options show this
behavior. "-pbc inbox" does keep the ligand in the same box, but it drifts
relative to the protein and jumps around, leading me to think that the wrapping
back into the simulation box isn't being handled correctly.
I have tried all of the different pbc options and can't get the desired
behavior (wrap the ligand -- which, for topology purposes, is part of the same
"molecule" as the protein -- into the same box as the protein CORRECTLY) to work
with any of them.
I am attaching a tpr and trr to reproduce the problem. This is in 3.3, although
the 3.3.1 patches version of trjconv appears to have the same problem.
#3 Updated by David Mobley about 13 years ago
I'll give the center option a shot, as I haven't tried it.
However, I'd suggest you try the
pbc inbox option: This is behaving mostly as
I'd like, except I think it is actually doing the wrapping into the box wrong -
that is, it must be making some errors as it wraps. The ligand seems to
translate with respect to the protein when I use the inbox option by a SMALL
distance, even though I know it's not doing so. This makes me think that the
routine that handles the periodicity has some kind of a bug.
#6 Updated by Berk Hess about 13 years ago
trjconv would never cause relative molecular motion of less than a box vector.
Could it be that one of your molecules is partially over a box edge?
trjconv -pbc inbox puts all atoms in the box and can therefore break molecules.
g_dist could then give the wrong center of mass if you did not supply
a tpr file.
I have just committed a fix for the 3.3 CVS version of trjconv.
If your molecules are broken the new -pbc mol option should solve your problem.
#7 Updated by David Mobley about 13 years ago
I'll have to try the changes out out, but could I perhaps suggest taking a look
at my trajectory? I DO use tpr's when I use g_dist; it seems to be working as I
expect -- the problem is just that the conversion to pdb gives "funny" results
as compared to g_dist (and, I might add, compared to ngmx).