How to optimize for Mpipi Model ? #1
Comments
|
Hi, sorry for the late reply, actually we have implemented Mpipi into OpenABC and will put it into the public repo soon. |
|
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
<#1 (comment)>,
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
|
|
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. |
|
An example is in tests/check-Mpipi |
|
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
<#1 (comment)>,
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
|
|
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 <module>
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
> <#1 (comment)>,
> 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
|
|
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 After I upload 1.0.4 version to pypi you can use |
|
I have just uploaded the newest version to pypi and you can update with command |
|
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
<#1 (comment)>,
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
|
|
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 <module>
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
> <#1 (comment)>,
> 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
|
|
Hi, thank you for pointing this out, I just uploaded the trajectory file to repo. |
|
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
<#1 (comment)>,
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
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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
The text was updated successfully, but these errors were encountered: