MDnalysis Discussion (ARCHIVED)

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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

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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?

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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).

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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

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<< 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,

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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>

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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?

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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

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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

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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

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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

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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

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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/

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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

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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

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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:

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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

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<< 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

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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.

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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.

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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

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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

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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

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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:

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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

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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

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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,

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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

isaac gimenez2

10/12/23

distance calculation from an atom to the COM

i have already solved! Thank you so much for posting it =) Isaac El dia dijous, 12 d'octubre de

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distance calculation from an atom to the COM

i have already solved! Thank you so much for posting it =) Isaac El dia dijous, 12 d'octubre de

10/12/23

Anuj Garg

10/11/23

SASA value

Hello all, I have recently started learning MD and MDAnalysis is very helpful. But I am not able to

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SASA value

Hello all, I have recently started learning MD and MDAnalysis is very helpful. But I am not able to

10/11/23

Dhanushka Weerakoon, … Oliver Beckstein6

10/9/23

Using MDAnalysis to calculate lipid-lipid hydrogen bonds in a membrane

Hi Dhanushka, Thank you for reporting what worked for you. This may be very helpful for anybody else

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Using MDAnalysis to calculate lipid-lipid hydrogen bonds in a membrane

Hi Dhanushka, Thank you for reporting what worked for you. This may be very helpful for anybody else

10/9/23