Dear Amber experts,
I just encountered a strange (at least to me) behaviour of the command
addionsrand in leap for identical systems (AmberTools23).
During system preparation, I created a unit containing a solvated
protein system; then I created three copies of it and wanted to randomly
add ions to the three independent systems. As it turned out, however,
leap seemed to use the same random numbers for all three systems, i.e.
it placed the ions at the same positions (same coordinates printed in
the log, and I diff'ed the pdb files: identical).
[...]
# solvated system stored in sys
sys1 = copy sys
sys2 = copy sys
sys3 = copy sys
# neutralize by adding ions randomly
addionsrand sys1 Na+ 0
addionsrand sys2 Na+ 0
addionsrand sys3 Na+ 0
# save systems with different ion positions
savepdb sys1 sys1.pdb
savepdb sys2 sys2.pdb
savepdb sys3 sys3.pdb
#
Is this the expected behaviour?
(I know that "random" on computer systems is an art of its own;
I'll use the randomizeions command in cpptraj then, but was happy to
find the leap command in the Amber manual.)
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
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Received on Fri Oct 06 2023 - 09:30:02 PDT
