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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
38 stars 26 forks source link

> Thanks for the report! That’s a bug on my part but I won’t have a computer for the next few weeks. You can get around it by adding the line `use_average_seq = 1` to your input file. #92

Closed Azzzzzz11 closed 3 months ago

Azzzzzz11 commented 3 months ago 
          > Thanks for the report! That’s a bug on my part but I won’t have a computer for the next few weeks. You can get around it by adding the line `use_average_seq = 1` to your input file.

Yes, I added the line use_average_seq = 1 in my input file. The above is the error after I added the average base. LOL~

Best regards, Yue

Originally posted by @HalseyWang in https://github.com/lorenzo-rovigatti/oxDNA/issues/56#issuecomment-1442713940

Azzzzzz11 commented 3 months ago

My input file =“input” I found it in folder “simulation” every time I put something I want to simulate， There will be a file called “input” in simulation. And I change“ use_average_seq=0” to “use_average_seq=1” ，it didnt work. After that， I check the input file，it recovered. Am I find a wrong input file. Could u help please？ BEST WISHES CHEN

lorenzo-rovigatti commented 3 months ago

It is not clear what you are asking. Can you please edit your post so that we can understand what's going on?

Azzzzzz11 commented 3 months ago

It is not clear what you are asking. Can you please edit your post so that we can understand what's going on?

Describe the situation 1.ERROR: Mandatory key `seq_dep_file' not found, exiting

I put the example into the website，there will be file ”input“ in the folder“simulation”. And I put ”use_ average_seq=1“into the ”input“ before running oxDNA. When I tried to run oxDNA，it‘s still will be ERROR: Mandatory key `seq_dep_file' not found, exiting， after that I check the changed file“input”，the line “use_average_seq=1“ disappeared. the file”input“ seems be
recovered.

  1. http://tacoxdna.sissa.it/Examples "Tiamat-oxDNA”

    Assuming DNA

    Assuming Tiamat version 2

    Traceback (most recent call last): File "/home/tacoxdna/git/tacoxDNA/src/Tiamat_oxDNA.py", line 453, in data = load(f_out) File "/usr/local/lib/python3.6/json/init.py", line 296, in load return loads(fp.read(), File "/usr/local/lib/python3.6/encodings/ascii.py", line 26, in decode return codecs.ascii_decode(input, self.errors)[0] UnicodeDecodeError: 'ascii' codec can't decode byte 0xff in position 0: ordinal not in range(128) Some errors have been detected, output not generated

Azzzzzz11 commented 3 months ago

It is not clear what you are asking. Can you please edit your post so that we can understand what's going on?

ok sir， and I’m sorry about that I’m a rookie of computer.

lorenzo-rovigatti commented 3 months ago

I'm sorry but this is still not very clear to me. I don't know what you are trying to do, nor how, and your post contains errors from oxDNA and tacoxDNA (which is a different software).

Azzzzzz11 commented 3 months ago

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Azzzzzz11 commented 3 months ago

I'm sorry but this is still not very clear to me. I don't know what you are trying to do, nor how, and your post contains errors from oxDNA and tacoxDNA (which is a different software). I put some pictures

lorenzo-rovigatti commented 3 months ago

I have the impression that you are not launching oxDNA yourself, but rather using other tools to do that. I've never used anything but the command line to launch oxDNA, so I can't help you here. You should refer to the people who built the tools you are using. @zoombya , maybe you can help us?

Azzzzzz11 commented 3 months ago

I have the impression that you are not launching oxDNA yourself, but rather using other tools to do that. I've never used anything but the command line to launch oxDNA, so I can't help you here. You should refer to the people who built the tools you are using. @zoombya , maybe you can help us?

ok I understand thank you！

ErikPoppleton commented 3 months ago

oxServe uses a pre-built input file and doesn't allow most options to be changed. This was done to make it streamlined for fast relaxation (it's not meant for production simulations). If you want full control over your simulations from a scripting interface, you should be using oxpy. @zoombya wrote a nice tutorial on simulation notebooks here

Azzzzzz11 commented 3 months ago

oxServe uses a pre-built input file and doesn't allow most options to be changed. This was done to make it streamlined for fast relaxation (it's not meant for production simulations). If you want full control over your simulations from a scripting interface, you should be using oxpy. @zoombya wrote a nice tutorial on simulation notebooks here

Thank you very much！ I will take a good look at this tutorial.