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lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
https://dna.physics.ox.ac.uk/
GNU General Public License v3.0
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Can't read configuration file from the examples [v3.6.1] #101

Closed A-VER closed 2 months ago

A-VER commented 2 months ago

Hello! After installing and compiling the oxDNA, I tried to ran examples but failed to read the configuration file. My code was like this: ./oxDNA ../examples/PSEUDOKNOT/inputMD1 And I got this: INFO: seeding the RNG with 764352577 INFO: Initializing backend INFO: Simulation type not specified, using MD INFO: The generator will try to take into account bonded interactions by choosing distances between bonded neighbours no larger than 2.000000 INFO: Converting temperature from Celsius (20.000000 C°) to simulation units (0.097717) INFO: Temperature change detected (new temperature: 20.00 C, 293.15 K), re-initialising the DNA interaction INFO: pid: 19960 INFO: Aggregated I/O statistics (set debug=1 for file-wise information) 0.000 B written to files 0.000 B written to stdout/stderr ERROR: Can't read configuration file 'generated.dat' After this I ran another two examples and got the same error. My installation process was like this: cd oxDNA-3.6.1 mkdir build cd build cmake -DPython=ON -DOxpySystemInstall=On -DG=ON -DINTEL=ON .. make -j16 And everything went ok. Does anyone know what is going on? Thanks very much for your help!

lorenzo-rovigatti commented 2 months ago

Hi! The examples should be run from their own folder. You should change directory and then run oxDNA there:

cd ../examples/PSEUDOKNOT/
../../build/bin/oxDNA inputMD1
A-VER commented 2 months ago

Hi! The examples should be run from their own folder. You should change directory and then run oxDNA there:

cd ../examples/PSEUDOKNOT/
../../build/bin/oxDNA inputMD1

Oh, I see! Thank you so much for helping!