Hi All,
Previously, there have been issues reported when attempting to
"unwrap" NPT trajectories (i.e. trajectories where the box size is
allowed to fluctuate) with CPPTRAJ, illustrated by an accumulation of
error in calculated diffusion constants that increases with increasing
trajectory length. This has recently been addressed in the GitHub
version of cpptraj (see
https://github.com/Amber-MD/cpptraj/pull/1027
and
https://github.com/Amber-MD/cpptraj/pull/1028) by forcing all
unwrapping to occur in fractional space, and adding the optional
'avgucell' keyword to unwrap to remove the effect of box fluctuations
by projecting coordinates back into Cartesian space via averaged unit
cell vectors. An example of this is:
parm tz2.ortho.parm7
trajin tz2.ortho.nc
# Calculate avg. box
avgbox MyBox
run
# Use avg box to remove fluctuations with unwrap
unwrap bymol avgucell MyBox[avg]
# Calculate diffusion; use noimage since coordinates are unwrapped
diffusion Water :WAT.O out tz2.ortho.wato.dat noimage
run
Note that this has not yet been ported to AmberTools 23 via a patch,
but I plan to do so as soon as I can. Let me know if there are any
questions.
-Dan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 12 2023 - 13:00:02 PDT
