Hi,
What happens if you invoke leap 3 different times (instead of having
all three "addionsrand" commands in a single script)? Same thing?
-Dan
On Fri, Oct 6, 2023 at 12:08 PM Dr. Anselm Horn via AMBER
<amber.ambermd.org> wrote:
>
> 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 Tue Oct 10 2023 - 06:30:04 PDT
