search

ZhangGroup-MITChemistry / OpenABC

OpenMM implementation of MOFF, MRG-CG, and HPS models.
MIT License
24 stars 4 forks source link

How to optimize for Mpipi Model ? #1

Open kesavanekambaram opened 1 year ago

kesavanekambaram commented 1 year ago

Hi, I am trying to run my condensate simulations using lammps with Mpipi model and recently came across your article reporting on the OpenABC to run condensate on OpenMM, which is great and I am interested to know how to optimize it for the Mpipi force field to run for the protein systems using the OpenABC? Please do help me out in this regard? Thank you

smliu1997 commented 1 year ago

Hi, sorry for the late reply, actually we have implemented Mpipi into OpenABC and will put it into the public repo soon.

kesavanekambaram commented 1 year ago

No issues. Thank you letting me know. Eagerly awaiting to check it out.

On Sat, 1 Jul 2023 at 12:41 AM Shuming Liu @.***> wrote:

Hi, sorry for the late reply, actually we have implemented Mpipi into OpenABC and will put it into the public repo soon.

— Reply to this email directly, view it on GitHub https://github.com/ZhangGroup-MITChemistry/OpenABC/issues/1#issuecomment-1615092939, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFZDTSR2MKIZJSWXLP67P3XN4QGVANCNFSM6AAAAAAYSNKXMM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Regards, Srinivasan E Research Associate Molecular Biophysics Unit (MBU) Indian Institute of Science Bengaluru - 560012 Karnataka, India https://sites.google.com/view/esrinivasan/home https://www.google.com/url?q=https://sites.google.com/view/esrinivasan/home&sa=D&source=hangouts&ust=1536036673520000&usg=AFQjCNGbT4E_pB_PrQ87nIiK7RxjuYQ3eA

உணலினும் உண்டது அறல்இனிது காமம் புணர்தலின் ஊடல் இனிது - திருவள்ளுவர்

smliu1997 commented 1 year ago

Hi, I have just uploaded the newest version 1.0.4 to github repo. You can download and try Mpipi model now! I will upload this to pypi later.

smliu1997 commented 1 year ago

An example is in tests/check-Mpipi

kesavanekambaram commented 1 year ago

Thanks, I'll check it out.

On Sat, 1 Jul 2023 at 2:27 AM Shuming Liu @.***> wrote:

An example is in tests/check-Mpipi

— Reply to this email directly, view it on GitHub https://github.com/ZhangGroup-MITChemistry/OpenABC/issues/1#issuecomment-1615189000, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFZDTXJRJQ7C27ME2BWM43XN44R5ANCNFSM6AAAAAAYSNKXMM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Regards, Srinivasan E Research Associate Molecular Biophysics Unit (MBU) Indian Institute of Science Bengaluru - 560012 Karnataka, India https://sites.google.com/view/esrinivasan/home https://www.google.com/url?q=https://sites.google.com/view/esrinivasan/home&sa=D&source=hangouts&ust=1536036673520000&usg=AFQjCNGbT4E_pB_PrQ87nIiK7RxjuYQ3eA

உணலினும் உண்டது அறல்இனிது காமம் புணர்தலின் ஊடல் இனிது - திருவள்ளுவர்

kesavanekambaram commented 1 year ago

Hi Liu, I tried with the Mpipi run after installation but ended with the error Traceback (most recent call last): File "/home/srinivasan/Downloads/OpenABC-main/tests/check-Mpipi_my_test/rerun.py", line 16, in from openabc.forcefields.parsers import MpipiProteinParser, MpipiRNAParser ImportError: cannot import name 'MpipiProteinParser' from 'openabc.forcefields.parsers' (/home/srinivasan/anaconda3/envs/openabc/lib/python3.9/site-packages/openabc/forcefields/parsers/init.py)

Could you help me out with this?

On Sat, Jul 1, 2023 at 8:43 AM Kesavan @.***> wrote:

Thanks, I'll check it out.

On Sat, 1 Jul 2023 at 2:27 AM Shuming Liu @.***> wrote:

An example is in tests/check-Mpipi

— Reply to this email directly, view it on GitHub https://github.com/ZhangGroup-MITChemistry/OpenABC/issues/1#issuecomment-1615189000, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFZDTXJRJQ7C27ME2BWM43XN44R5ANCNFSM6AAAAAAYSNKXMM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Regards, Srinivasan E Research Associate Molecular Biophysics Unit (MBU) Indian Institute of Science Bengaluru - 560012 Karnataka, India https://sites.google.com/view/esrinivasan/home https://www.google.com/url?q=https://sites.google.com/view/esrinivasan/home&sa=D&source=hangouts&ust=1536036673520000&usg=AFQjCNGbT4E_pB_PrQ87nIiK7RxjuYQ3eA

உணலினும் உண்டது அறல்இனிது காமம் புணர்தலின் ஊடல் இனிது - திருவள்ளுவர்

-- With Regards, Srinivasan E Research Associate Molecular Biophysics Unit (MBU) Indian Institute of Science Bengaluru - 560012 Karnataka, India https://sites.google.com/view/esrinivasan/home https://www.google.com/url?q=https://sites.google.com/view/esrinivasan/home&sa=D&source=hangouts&ust=1536036673520000&usg=AFQjCNGbT4E_pB_PrQ87nIiK7RxjuYQ3eA

உணலினும் உண்டது அறல்இனிது காமம் புணர்தலின் ஊடல் இனிது - திருவள்ளுவர்

smliu1997 commented 1 year ago

It looks like you are still using openabc installed in this environment, instead of the one in this repo. As I have not uploaded 1.0.4 version to pypi yet, the one you are actually using is not the 1.0.4 version. You can either set up a new environment and use sys.path.append to append the path for the up-to-date version of openabc, or you can just pip uninstall openabc to uninstall the one installed with pip, then append the path of 1.0.4 version of openabc.

After I upload 1.0.4 version to pypi you can use pip install openabc -U to install or update the newest version.

smliu1997 commented 1 year ago

I have just uploaded the newest version to pypi and you can update with command pip install openabc -U, then try running the script again.

kesavanekambaram commented 1 year ago

Awesome Thanks. I will check it out.

On Sun, 2 Jul 2023 at 2:50 AM Shuming Liu @.***> wrote:

I have just uploaded the newest version to pypi and you can update with command pip install openabc -U, then try running the script again.

— Reply to this email directly, view it on GitHub https://github.com/ZhangGroup-MITChemistry/OpenABC/issues/1#issuecomment-1616136384, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFZDTTIGKURIS5WPVNWPBLXOCIARANCNFSM6AAAAAAYSNKXMM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Regards, Srinivasan E Research Associate Molecular Biophysics Unit (MBU) Indian Institute of Science Bengaluru - 560012 Karnataka, India https://sites.google.com/view/esrinivasan/home https://www.google.com/url?q=https://sites.google.com/view/esrinivasan/home&sa=D&source=hangouts&ust=1536036673520000&usg=AFQjCNGbT4E_pB_PrQ87nIiK7RxjuYQ3eA

உணலினும் உண்டது அறல்இனிது காமம் புணர்தலின் ஊடல் இனிது - திருவள்ளுவர்

kesavanekambaram commented 1 year ago

Hi, I tried running the test for Mpipi model but the lammps dump folder doesn't have the trajectory file I created by running it in my system. Still, I am facing the issue of Traceback (most recent call last): File "/home/srinivasan/Downloads/OpenABC-main/tests/check-Mpipi_my_test/rerun.py", line 74, in assert np.amax(diff) <= 0.01 AssertionError Could you please chek it out?

On Sun, Jul 2, 2023 at 3:31 AM Kesavan @.***> wrote:

Awesome Thanks. I will check it out.

On Sun, 2 Jul 2023 at 2:50 AM Shuming Liu @.***> wrote:

I have just uploaded the newest version to pypi and you can update with command pip install openabc -U, then try running the script again.

— Reply to this email directly, view it on GitHub https://github.com/ZhangGroup-MITChemistry/OpenABC/issues/1#issuecomment-1616136384, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFZDTTIGKURIS5WPVNWPBLXOCIARANCNFSM6AAAAAAYSNKXMM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Regards, Srinivasan E Research Associate Molecular Biophysics Unit (MBU) Indian Institute of Science Bengaluru - 560012 Karnataka, India https://sites.google.com/view/esrinivasan/home https://www.google.com/url?q=https://sites.google.com/view/esrinivasan/home&sa=D&source=hangouts&ust=1536036673520000&usg=AFQjCNGbT4E_pB_PrQ87nIiK7RxjuYQ3eA

உணலினும் உண்டது அறல்இனிது காமம் புணர்தலின் ஊடல் இனிது - திருவள்ளுவர்

-- With Regards, Srinivasan E Research Associate Molecular Biophysics Unit (MBU) Indian Institute of Science Bengaluru - 560012 Karnataka, India https://sites.google.com/view/esrinivasan/home https://www.google.com/url?q=https://sites.google.com/view/esrinivasan/home&sa=D&source=hangouts&ust=1536036673520000&usg=AFQjCNGbT4E_pB_PrQ87nIiK7RxjuYQ3eA

உணலினும் உண்டது அறல்இனிது காமம் புணர்தலின் ஊடல் இனிது - திருவள்ளுவர்

smliu1997 commented 1 year ago

Hi, thank you for pointing this out, I just uploaded the trajectory file to repo.

kesavanekambaram commented 1 year ago

Awesome, thank you so much!

On Wed, Jul 5, 2023 at 4:41 AM Shuming Liu @.***> wrote:

Hi, thank you for pointing this out, I just uploaded the trajectory file to repo.

— Reply to this email directly, view it on GitHub https://github.com/ZhangGroup-MITChemistry/OpenABC/issues/1#issuecomment-1620818870, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGFZDTUSOQ2K4OJDEII4AULXOSPIPANCNFSM6AAAAAAYSNKXMM . You are receiving this because you authored the thread.Message ID: @.***>

-- With Regards, Srinivasan E Research Associate Molecular Biophysics Unit (MBU) Indian Institute of Science Bengaluru - 560012 Karnataka, India https://sites.google.com/view/esrinivasan/home https://www.google.com/url?q=https://sites.google.com/view/esrinivasan/home&sa=D&source=hangouts&ust=1536036673520000&usg=AFQjCNGbT4E_pB_PrQ87nIiK7RxjuYQ3eA

உணலினும் உண்டது அறல்இனிது காமம் புணர்தலின் ஊடல் இனிது - திருவள்ளுவர்