MDnalysis Discussion (ARCHIVED)

Contact owners and managers

1–30 of 1313

Welcome!

This is an archive of the MDAnalysis Discussion mailing list. Please use GitHub Discussions instead.

In addition to the project homepage see also the full Online Documentation for more information.

0 selected

Y. W, Oliver Beckstein2

Nov 8

ModuleNotFoundError: No module named 'MDAnalysis.analysis.atomicdistances'

Hello Yuhan, We're not using this mailing list anymore. Please see https://www.mdanalysis.org/#

unread,

ModuleNotFoundError: No module named 'MDAnalysis.analysis.atomicdistances'

Hello Yuhan, We're not using this mailing list anymore. Please see https://www.mdanalysis.org/#

Nov 8

Viswanath Vittaladevaram, Richard Gowers3

Jun 12

gromacs to amber files conversion : Parmed exception.Gromacs error: No template defined

Hi, I am finding this error mentioned below Using 1 MPI thread Using 12 OpenMP threads WARNING: This

unread,

gromacs to amber files conversion : Parmed exception.Gromacs error: No template defined

Hi, I am finding this error mentioned below Using 1 MPI thread Using 12 OpenMP threads WARNING: This

Jun 12

Aashish Bhatt, … Richard Gowers4

May 14

Regarding Lammps trajectroy

Hi Aashish That's a confusing error as it looks like it expects 5 values but the style you

unread,

Regarding Lammps trajectroy

Hi Aashish That's a confusing error as it looks like it expects 5 values but the style you

May 14

aj...@nyu.edu, Project Manager MDAnalysis4

Feb 28

Hydrogen Bond Analysis of water; error

Hi Alexej, I'm glad that you were able to figure out the issue. In future, please also note that

unread,

Hydrogen Bond Analysis of water; error

Hi Alexej, I'm glad that you were able to figure out the issue. In future, please also note that

Feb 28

Yogesh Sharma, Lily Wang6

12/29/23

Producing a colored dot surface using mdanalysis hole over a trajectory

Dear Yogesh, We have now moved to GitHub Discussions — could you please ask your question there?

unread,

Producing a colored dot surface using mdanalysis hole over a trajectory

Dear Yogesh, We have now moved to GitHub Discussions — could you please ask your question there?

12/29/23

Maria Thereza, Rocco Meli2

12/28/23

MSD and self-diffusivity of water

Hi Maria, We are retiring the mailing list and moving to GitHub discussions (blog post to come soon).

unread,

MSD and self-diffusivity of water

Hi Maria, We are retiring the mailing list and moving to GitHub discussions (blog post to come soon).

12/28/23

I. Camps, Rocco Meli4

12/21/23

<< PDBWriter parameters >>

Thank you! I replied to you there. Best, Rocco On Thursday, December 21, 2023 at 4:11:09 PM UTC+1 ica

unread,

<< PDBWriter parameters >>

Thank you! I replied to you there. Best, Rocco On Thursday, December 21, 2023 at 4:11:09 PM UTC+1 ica

12/21/23

Rocco Meli

12/20/23

Moving to GitHub Discussions

Dear MDAnalysis community, Our Google groups have been the main way to ask questions, exchange ideas,

unread,

Moving to GitHub Discussions

Dear MDAnalysis community, Our Google groups have been the main way to ask questions, exchange ideas,

12/20/23

DULAL MONDAL2

12/20/23

Mean square displacement calculation of active site water molecules

please any help. On Wed, Dec 20, 2023 at 4:13 PM DULAL MONDAL <babunmon...@gmail.com>

unread,

Mean square displacement calculation of active site water molecules

please any help. On Wed, Dec 20, 2023 at 4:13 PM DULAL MONDAL <babunmon...@gmail.com>

12/20/23

DULAL MONDAL

12/18/23

How to calculate entrop of active site water molecules

Dear Experts, Can anyone please help me calculate the entropy of active site water molecules?

unread,

How to calculate entrop of active site water molecules

Dear Experts, Can anyone please help me calculate the entropy of active site water molecules?

12/18/23

Maria Thereza, Oliver Beckstein2

12/15/23

Distances on MDAnalysis

Hi Maria, On Dec 15, 2023, at 07:54, Maria Thereza <mariath...@gmail.com> wrote: Hi

unread,

Distances on MDAnalysis

Hi Maria, On Dec 15, 2023, at 07:54, Maria Thereza <mariath...@gmail.com> wrote: Hi

12/15/23

fardine ameli

12/5/23

Selections

Hello everyone Is there a way to select "residue" in MDAnalysis, similar to the

unread,

Selections

Hello everyone Is there a way to select "residue" in MDAnalysis, similar to the

12/5/23

aj...@nyu.edu, Oliver Beckstein3

11/30/23

rdf normalization confusion

Super, thank you. The problem was the old documentation. When I use norm='none', it seems I

unread,

rdf normalization confusion

Super, thank you. The problem was the old documentation. When I use norm='none', it seems I

11/30/23

Margaret Brooks, Micaela Matta3

11/30/23

MDA diffusisivty vs. LAMMPS diffusivity

HI, sorry for the delay; I thought I had replied but it appears it didn't go through. I'll

unread,

MDA diffusisivty vs. LAMMPS diffusivity

HI, sorry for the delay; I thought I had replied but it appears it didn't go through. I'll

11/30/23

Maria Thereza, Hugo Macdermott-Opeskin4

11/30/23

Coordination number of a molecule

Hello Hugo, First of all thank you very much for your advice on using Solvation Analysis! I've

unread,

Coordination number of a molecule

Hello Hugo, First of all thank you very much for your advice on using Solvation Analysis! I've

11/30/23

Joan Garcia i Masferrer

11/30/23

Atomselection in sphlayer and sphzone non consistent

Hy everyone. Im working on a project where I need to calculate the radial density of a set compound/

unread,

Atomselection in sphlayer and sphzone non consistent

Hy everyone. Im working on a project where I need to calculate the radial density of a set compound/

11/30/23

Aashish Bhatt, Oliver Beckstein2

11/21/23

MDA diffusivity

Hello Aashish, welcome to the MDAnalysis mailing list! You can use MDAnalysis to see what the time

unread,

MDA diffusivity

Hello Aashish, welcome to the MDAnalysis mailing list! You can use MDAnalysis to see what the time

11/21/23

Maria Thereza, Micaela Matta2

11/14/23

Question about hydrogen bonding calculation

Hi Maria, what options did you use when calling HydrogenBondAnalysis? What do you see when looking at

unread,

Question about hydrogen bonding calculation

Hi Maria, what options did you use when calling HydrogenBondAnalysis? What do you see when looking at

11/14/23

Paolus, Micaela Matta2

11/14/23

How to add an atom to a residue of a given universe, ore replace a residue

Hi Paulus, yes, it's possible to modify atoms in a Universe. Have a look at the examples here:

unread,

How to add an atom to a residue of a given universe, ore replace a residue

Hi Paulus, yes, it's possible to modify atoms in a Universe. Have a look at the examples here:

11/14/23

I. Camps, Hugo Macdermott-Opeskin3

11/13/23

<< Adding charges to PDB >>

Thank you very much. But I needed to add the charge in the correct place, as a third-party

unread,

<< Adding charges to PDB >>

Thank you very much. But I needed to add the charge in the correct place, as a third-party

11/13/23

Project Manager MDAnalysis, jules epee3

11/13/23

Towards MDAnalysis 3.0

Dear Jules, Thank you for your interest in becoming a maintainer for an MDAKit and participating in

unread,

Towards MDAnalysis 3.0

Dear Jules, Thank you for your interest in becoming a maintainer for an MDAKit and participating in

11/13/23

Jason Held, Hugo Macdermott-Opeskin4

11/1/23

Structural inconsistencies, at least partially related to traj length

Sorry, that last 'view' should be alone on the last line, but there was a formatting hiccup.

unread,

Structural inconsistencies, at least partially related to traj length

Sorry, that last 'view' should be alone on the last line, but there was a formatting hiccup.

11/1/23

DULAL MONDAL, Oliver Beckstein2

10/31/23

Dielectric constant

Hi Dulal, I suggest you have a look at MAICoS for more advanced calculations, see https://maicos.

unread,

Dielectric constant

Hi Dulal, I suggest you have a look at MAICoS for more advanced calculations, see https://maicos.

10/31/23

Maria Thereza, Hugo Macdermott-Opeskin4

10/26/23

MSD calculation

Hi Maria, would you be able to check that the arrays are binary identical rather than just look

unread,

MSD calculation

Hi Maria, would you be able to check that the arrays are binary identical rather than just look

10/26/23

Maria Thereza, Fiona Naughton3

10/25/23

RMSD Calculation

Hello Fiona, Thank you very much! It worked by putting reference instead of ref, silly me. Have a

unread,

RMSD Calculation

Hello Fiona, Thank you very much! It worked by putting reference instead of ref, silly me. Have a

10/25/23

Project Manager MDAnalysis

10/24/23

Invitation for Oct 25 MDAnalysis Online Workshop

Dear MDAnalysis Users, We still have slots available for our first MDAnalysis Online Workshop, taking

unread,

Invitation for Oct 25 MDAnalysis Online Workshop

Dear MDAnalysis Users, We still have slots available for our first MDAnalysis Online Workshop, taking

10/24/23

Srdjan Pusara, Oliver Beckstein6

10/19/23

Hydrogen bond analysis error - AttributeError: 'int' object has no attribute 'positions'

If it will be helpful, I can share my MD trajectory files and python code. On Thu, 19 Oct 2023 at 15:

unread,

Hydrogen bond analysis error - AttributeError: 'int' object has no attribute 'positions'

If it will be helpful, I can share my MD trajectory files and python code. On Thu, 19 Oct 2023 at 15:

10/19/23

Sanjeet Singh, Hugo Macdermott-Opeskin2

10/17/23

Regarding convention for dihedral angle

Hi Sanjeet, MDAnalysis returns dihedrals in terms of angles. You can then compare these to the

unread,

Regarding convention for dihedral angle

Hi Sanjeet, MDAnalysis returns dihedrals in terms of angles. You can then compare these to the

10/17/23

Maria Thereza, Hugo Macdermott-Opeskin2

10/17/23

Hydrogen bonding analysis

Hi Maria Looks to me like you are incorporating solvent-solvent hydrogen bonds in your second example

unread,

Hydrogen bonding analysis

Hi Maria Looks to me like you are incorporating solvent-solvent hydrogen bonds in your second example

10/17/23

Satyen Dhamankar, Roshan Shrestha2

10/17/23

Where does the Universe object store the dimensions of the simulation cell?

Hi, You can access the dimensions at Universe.trajectory.dimensions With best regards On Tue, Oct 17,

unread,

Where does the Universe object store the dimensions of the simulation cell?

Hi, You can access the dimensions at Universe.trajectory.dimensions With best regards On Tue, Oct 17,

10/17/23