Using MDAnalysis in windows

[hanahg]

Hi,

I tried to use MDAnalysis from Anaconda Windows environment. Like Linux, I installed and activated it, but I saw after opening Jupyter note book and try to run my codes, MDAnalysis did not recognized: No module named 'MDAnalysis.
I do not know how to find the problem and resolve it.
Thank you for your helps and wish you a wonderful new year

[hmacdope]

Hi. Would you be able to show exactly how you installed MDAnalysis? Does MDAnalysis appear when you run conda list?

[IAlibay]

That's ok, you should still be able to paste it here.

[hanahg]

I tried but could not.

[IAlibay]

Could you maybe drop it here as a file?

[hanahg]

I don't know.
Now using windows id not my priority. The priority is working on script that I explained in another discussion. I mean calculating the electrostatic charge of Np from the center of GNP to the end and plotting the results.

[hanahg]

I am using MDAnalysis on linux at the university, I need to think about on my windows when I am home and I have no access to the linux.

[orbeckst]

Did you install jupyter inside your conda environment?

[hanahg]

yes, and it woks but not mdanalysis inside of it

[hanahg]

Yes, I opened Anaconda inside the working folder, activated the MDAnalysis then opened Jupyter notebook. Inside Jupiter notebook, the commad of importing MDAnalysis as mda did not work. Sent from Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Oliver Beckstein ***@***.***> Sent: Thursday, January 4, 2024 12:37:05 AM To: MDAnalysis/mdanalysis ***@***.***> Cc: hanahg ***@***.***>; Author ***@***.***> Subject: Re: [MDAnalysis/mdanalysis] Using MDAnalysis in windows (Discussion #4406) Did you install jupyter inside your conda environment? — Reply to this email directly, view it on GitHub<#4406 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AI5LF65QOXIOTZAPLRDAI7TYMXTSDAVCNFSM6AAAAABBMEFUACVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DAMBXHA3DG>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[orbeckst]

I am using macOS or Linux so I don't know how to use the Windows GUI version. Maybe someone else knows more.

In macOS/Linux I exclusively use the command line, e.g.(see also the Installation Guide)

conda config --add channels conda-forge
conda create --name mdanalysis python=3.11  # environment named mdanalysis based on Python 3.11
conda activate mdanalysis
conda install mamba                         # faster conda (not necessary, you can just use conda)
mamba install mdanalysis mdanalysistests    # install MDAnalysis
mamba install jupyter                       # install jupyter INSIDE the mdanalysis env!!!

When I want to work in this environment I will run

conda activate mdanalysis
jupyter-lab

Inside jupyter-lab I can import MDAnalysis.

[hanahg]

```console C:\Users\fatem>conda list # packages in environment at C:\Users\fatem\anaconda3: # # Name Version Build Channel _ipyw_jlab_nb_ext_conf 0.1.0 py39haa95532_0 _r-mutex 1.0.1 anacondar_1 conda-forge alabaster 0.7.12 pyhd3eb1b0_0 anaconda 2022.10 py39_0 anaconda-anon-usage 0.4.3 py39h8ddfbff_0 anaconda-client 1.11.0 py39haa95532_0 anaconda-cloud-auth 0.1.4 pyhd8ed1ab_0 conda-forge anaconda-navigator 2.5.0 py39haa95532_0 anaconda-project 0.11.1 py39haa95532_0 anyio 3.5.0 py39haa95532_0 appdirs 1.4.4 pyhd3eb1b0_0 argon2-cffi 21.3.0 pyhd3eb1b0_0 argon2-cffi-bindings 21.2.0 py39h2bbff1b_0 arrow 1.2.2 pyhd3eb1b0_0 astroid 2.11.7 py39haa95532_0 astropy 5.1 py39h080aedc_0 astunparse 1.6.3 pyhd8ed1ab_0 conda-forge atomicwrites 1.4.0 py_0 attrs 21.4.0 pyhd3eb1b0_0 automat 20.2.0 py_0 autopep8 1.6.0 pyhd3eb1b0_1 babel 2.9.1 pyhd3eb1b0_0 backcall 0.2.0 pyhd3eb1b0_0 backports 1.1 pyhd3eb1b0_0 backports.functools_lru_cache 1.6.4 pyhd3eb1b0_0 backports.tempfile 1.0 pyhd3eb1b0_1 backports.weakref 1.0.post1 py_1 backports.zoneinfo 0.2.1 py39hcbf5309_8 conda-forge bcrypt 3.2.0 py39h2bbff1b_1 beautifulsoup4 4.11.1 py39haa95532_0 binaryornot 0.4.4 pyhd3eb1b0_1 biopython 1.81 pypi_0 pypi bitarray 2.5.1 py39h2bbff1b_0 bkcharts 0.2 py39haa95532_1 black 22.6.0 py39haa95532_0 blas 1.0 mkl bleach 4.1.0 pyhd3eb1b0_0 blosc 1.21.0 h19a0ad4_1 bokeh 2.4.3 py39haa95532_0 boltons 23.1.1 pyhd8ed1ab_0 conda-forge boost 1.74.0 py39hefe7e4c_5 conda-forge boost-cpp 1.74.0 h5b4e17d_6 conda-forge boto3 1.24.28 py39haa95532_0 botocore 1.27.28 py39haa95532_0 bottleneck 1.3.5 py39h080aedc_0 brotli 1.0.9 h2bbff1b_7 brotli-bin 1.0.9 h2bbff1b_7 brotlipy 0.7.0 py39h2bbff1b_1003 bzip2 1.0.8 he774522_0 ca-certificates 2022.07.19 haa95532_0 anaconda cairo 1.16.0 he04af86_2 certifi 2022.9.14 py39haa95532_0 anaconda cffi 1.15.1 py39h2bbff1b_0 cfitsio 3.470 h2bbff1b_7 cftime 1.6.2 py39h080aedc_0 chardet 4.0.0 py39haa95532_1003 charls 2.2.0 h6c2663c_0 charset-normalizer 2.0.4 pyhd3eb1b0_0 click 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conda-forge rope 0.22.0 pyhd3eb1b0_0 rtree 0.9.7 py39h2eaa2aa_1 ruamel.yaml 0.17.21 py39hb82d6ee_1 conda-forge ruamel.yaml.clib 0.2.6 py39h2bbff1b_1 anaconda ruamel_yaml 0.15.100 py39h2bbff1b_0 s3transfer 0.6.0 py39haa95532_0 scikit-image 0.19.2 py39hf11a4ad_0 scikit-learn 1.0.2 py39hf11a4ad_1 scikit-learn-intelex 2021.6.0 py39haa95532_0 scipy 1.9.1 py39he11b74f_0 scrapy 2.6.2 py39haa95532_0 seaborn 0.11.2 pyhd3eb1b0_0 selfies 2.1.1 pypi_0 pypi semver 3.0.2 pyhd8ed1ab_0 conda-forge send2trash 1.8.0 pyhd3eb1b0_1 service_identity 18.1.0 pyhd3eb1b0_1 setuptools 63.4.1 py39haa95532_0 sip 4.19.13 py39hd77b12b_0 six 1.16.0 pyhd3eb1b0_1 smart_open 5.2.1 py39haa95532_0 snappy 1.1.9 h6c2663c_0 sniffio 1.2.0 py39haa95532_1 snowballstemmer 2.2.0 pyhd3eb1b0_0 sortedcollections 2.1.0 pyhd3eb1b0_0 sortedcontainers 2.4.0 pyhd3eb1b0_0 soupsieve 2.3.1 pyhd3eb1b0_0 sphinx 5.0.2 py39haa95532_0 sphinxcontrib-applehelp 1.0.2 pyhd3eb1b0_0 sphinxcontrib-devhelp 1.0.2 pyhd3eb1b0_0 sphinxcontrib-htmlhelp 2.0.0 pyhd3eb1b0_0 sphinxcontrib-jsmath 1.0.1 pyhd3eb1b0_0 sphinxcontrib-qthelp 1.0.3 pyhd3eb1b0_0 sphinxcontrib-serializinghtml 1.1.5 pyhd3eb1b0_0 spyder 5.2.2 py39haa95532_1 spyder-kernels 2.2.1 py39haa95532_0 sqlalchemy 1.4.39 py39h2bbff1b_0 sqlite 3.39.3 h2bbff1b_0 statsmodels 0.13.2 py39h2bbff1b_0 sympy 1.10.1 py39haa95532_0 tabulate 0.8.10 py39haa95532_0 tbb 2021.6.0 h59b6b97_0 tbb4py 2021.6.0 py39h59b6b97_0 tblib 1.7.0 pyhd3eb1b0_0 tenacity 8.0.1 py39haa95532_1 terminado 0.13.1 py39haa95532_0 testpath 0.6.0 py39haa95532_0 text-unidecode 1.3 pyhd3eb1b0_0 textdistance 4.2.1 pyhd3eb1b0_0 threadpoolctl 2.2.0 pyh0d69192_0 three-merge 0.1.1 pyhd3eb1b0_0 tidynamics 1.1.2 pyhd8ed1ab_0 conda-forge tifffile 2021.7.2 pyhd3eb1b0_2 tinycss 0.4 pyhd3eb1b0_1002 tk 8.6.12 h2bbff1b_0 tldextract 3.2.0 pyhd3eb1b0_0 toml 0.10.2 pyhd3eb1b0_0 tomli 2.0.1 py39haa95532_0 tomlkit 0.11.1 py39haa95532_0 toolz 0.11.2 pyhd3eb1b0_0 tornado 6.1 py39h2bbff1b_0 tqdm 4.64.1 py39haa95532_0 traitlets 5.1.1 pyhd3eb1b0_0 twisted 22.2.0 py39h2bbff1b_1 twisted-iocpsupport 1.0.2 py39h2bbff1b_0 typing-extensions 4.3.0 py39haa95532_0 typing_extensions 4.3.0 py39haa95532_0 tzdata 2022c h04d1e81_0 ujson 5.4.0 py39hd77b12b_0 unidecode 1.2.0 pyhd3eb1b0_0 urllib3 1.26.11 py39haa95532_0 vc 14.2 h21ff451_1 vs2015_runtime 14.27.29016 h5e58377_2 w3lib 1.21.0 pyhd3eb1b0_0 watchdog 2.1.6 py39haa95532_0 wcwidth 0.2.5 pyhd3eb1b0_0 webencodings 0.5.1 py39haa95532_1 websocket-client 0.58.0 py39haa95532_4 werkzeug 2.0.3 pyhd3eb1b0_0 wheel 0.37.1 pyhd3eb1b0_0 widget-jsmol 2.0.0 pypi_0 pypi widgetsnbextension 3.5.2 py39haa95532_0 win_inet_pton 1.1.0 py39haa95532_0 win_unicode_console 0.5 py39haa95532_0 wincertstore 0.2 py39haa95532_2 winpty 0.4.3 4 conda-forge wrapt 1.14.1 py39h2bbff1b_0 xarray 0.20.1 pyhd3eb1b0_1 xlrd 2.0.1 pyhd3eb1b0_0 xlsxwriter 3.0.3 pyhd3eb1b0_0 xlwings 0.27.15 py39haa95532_0 xz 5.2.6 h8cc25b3_0 yaml 0.2.5 he774522_0 conda-forge yapf 0.31.0 pyhd3eb1b0_0 yellowbrick 1.5 pypi_0 pypi zeromq 4.3.4 hd77b12b_0 zfp 0.5.5 hd77b12b_6 zict 2.1.0 py39haa95532_0 zipp 3.8.0 py39haa95532_0 zlib 1.2.12 h8cc25b3_3 zope 1.0 py39haa95532_1 zope.interface 5.4.0 py39h2bbff1b_0 zstandard 0.19.0 py39h2bbff1b_0 zstd 1.5.2 h19a0ad4_0 ``` Envoyé à partir de Outlook<http://aka.ms/weboutlook>

…

________________________________ From: Irfan Alibay ***@***.***> Sent: Tuesday, January 9, 2024 3:42 PM To: MDAnalysis/mdanalysis ***@***.***> Cc: hanahg ***@***.***>; Mention ***@***.***> Subject: Re: [MDAnalysis/mdanalysis] Using MDAnalysis in windows (Discussion #4406) @hanahg<https://github.com/hanahg> as per @hmacdope<https://github.com/hmacdope>'s suggestion, could you give us the output of conda list? — Reply to this email directly, view it on GitHub<#4406 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AI5LF64HSCYMCMDHORBG5Z3YNVJNZAVCNFSM6AAAAABBMEFUACVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DANRXGUYDC>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[nataliyah123]

i have not made any python environment on windows. just directly tested the working of mdanalysis in Jupyter, its working.
. Hope this can help you.