PLUMED users - Google Groups

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Mandar Kulkarni, Giovanni Bussi4

Aug 12

eRMSD on modified nucleotides

Is it possible to choose different base atoms other than C2, C4, and C6? Best Regards, Mandar

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eRMSD on modified nucleotides

Is it possible to choose different base atoms other than C2, C4, and C6? Best Regards, Mandar

Aug 12

Aug 4

Serious performance regression and potential LOCAL_AVERAGE bug in PLUMED 2.10 with GROMACS 2023.5

Dear PLUMED developers, I am writing to report a significant performance issue and a potential bug

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Serious performance regression and potential LOCAL_AVERAGE bug in PLUMED 2.10 with GROMACS 2023.5

Dear PLUMED developers, I am writing to report a significant performance issue and a potential bug

Aug 4

Mandar Kulkarni2

Jun 28

Plumed pyx and installation issue

Changing line type to int, solved the problem. Changed line 232 of python/plumed.pyx (plumed 2.9.0)

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Plumed pyx and installation issue

Changing line type to int, solved the problem. Changed line 232 of python/plumed.pyx (plumed 2.9.0)

Jun 28

Jun 26

Dependence on PBC corrections

Hello, i am a beginner in learning post trajectory analysis and i have a question. do global

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Dependence on PBC corrections

Hello, i am a beginner in learning post trajectory analysis and i have a question. do global

Jun 26

Jun 17

Loops in Plumed?

I have a group in a .ndx file and would like to apply a restraint to each atom individually in the

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Loops in Plumed?

I have a group in a .ndx file and would like to apply a restraint to each atom individually in the

Jun 17

Jun 11

Research Technologist / Scientific Software Engineer Position at SISSA

Dear Colleagues and Friends, I have the opportunity to recruit a research technologist (scientific

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Research Technologist / Scientific Software Engineer Position at SISSA

Dear Colleagues and Friends, I have the opportunity to recruit a research technologist (scientific

Jun 11

Jun 5

Hello, I have been using ZDISTANCE CV to calculate the number of contacts between the CAs of a

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Hello, I have been using ZDISTANCE CV to calculate the number of contacts between the CAs of a

Jun 5

AASHIMA AASHIMA

Jun 5

Lechner - Dellago order parameter.

Dear all, I am trying to calculate Lechner - Dellago order parameter using plumed, and I am a little

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Lechner - Dellago order parameter.

Dear all, I am trying to calculate Lechner - Dellago order parameter using plumed, and I am a little

Jun 5

matteo ceccarelli, Giovanni Bussi2

Apr 28

gromacs 2025 with blackwell GPU

Ciao Matteo! At this stage I confirm that you should use older GROMACS versions. We don't have

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gromacs 2025 with blackwell GPU

Ciao Matteo! At this stage I confirm that you should use older GROMACS versions. We don't have

Apr 28

Apr 27

~4000x slowdown when biasing CVs from a 1600x1600 distance matrix

Dear PLUMED users/developers, We are encountering a severe performance issue when using PLUMED

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~4000x slowdown when biasing CVs from a 1600x1600 distance matrix

Dear PLUMED users/developers, We are encountering a severe performance issue when using PLUMED

Apr 27

Qinghua Liao, Giovanni Bussi7

Apr 17

high energy gap in HREX simulation, no exchange

Hello, I managed to install Gromacs 2021.5 patched with Plumed 2.7.0. I tried to run the simulation

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high energy gap in HREX simulation, no exchange

Hello, I managed to install Gromacs 2021.5 patched with Plumed 2.7.0. I tried to run the simulation

Apr 17

Jamil, Gareth Tribello3

Mar 20

Combining multiple variables in CENTER_OF_MULTICOLVAR

Hi, thanks for the detailed explanation, that helps a lot. What I want is to compute a single center

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Combining multiple variables in CENTER_OF_MULTICOLVAR

Hi, thanks for the detailed explanation, that helps a lot. What I want is to compute a single center

Mar 20

Feb 5

PLUMED on workstation with NVidia RTX 5090 graphics card

I'm considering buying a workstation with NVidia RTX 5090 graphics card (and AMD Ryzen CPU). If

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PLUMED on workstation with NVidia RTX 5090 graphics card

I'm considering buying a workstation with NVidia RTX 5090 graphics card (and AMD Ryzen CPU). If

Feb 5

Giovanni Bussi, Carlos Henrique2

Feb 4

Re: [plumed-users] Differences in ALPHARMSD values using MetaD and RESTRAINTS

Hi Giovanni, Thank you for your reply. Yes, METAD and RESTRAINT simulations of the same system using

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Re: [plumed-users] Differences in ALPHARMSD values using MetaD and RESTRAINTS

Hi Giovanni, Thank you for your reply. Yes, METAD and RESTRAINT simulations of the same system using

Feb 4

Qinghua Liao, Giovanni Bussi3

Feb 2

confused distance units when processing xyz file with plumed driver

Thanks Prof. Bussi! Now I get it. All the best, Qinghua On Monday, February 2, 2026 at 6:16:25 PM UTC

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confused distance units when processing xyz file with plumed driver

Thanks Prof. Bussi! Now I get it. All the best, Qinghua On Monday, February 2, 2026 at 6:16:25 PM UTC

Feb 2

Carlos Henrique, Gareth Tribello2

Jan 21

non-periodic torsions

You could do this: t: TORSION ATOMS=1,2,3,4 c: CUSTOM ARG=t FUNC=x PERIODIC=NO You then use c in

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non-periodic torsions

You could do this: t: TORSION ATOMS=1,2,3,4 c: CUSTOM ARG=t FUNC=x PERIODIC=NO You then use c in

Jan 21

Jan 15

Umbrella samplling

Hello everyone, I am working with a porphyrin-like ligand bound in the active site of a protein. I

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Umbrella samplling

Hello everyone, I am working with a porphyrin-like ligand bound in the active site of a protein. I

Jan 15

jerryt...@gmail.com

12/18/25

Reweighting a WT-Metad simulation

Dear Forum, My apologies for the long message. I have done the metadynamics tutorial 21.4 and would

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Reweighting a WT-Metad simulation

Dear Forum, My apologies for the long message. I have done the metadynamics tutorial 21.4 and would

12/18/25

Glen Hocky, Giovanni Bussi2

12/15/25

RMSD without alignment?

Hi Glen Can you just use RMSD with different sets of atoms in the align and displace weights (two

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RMSD without alignment?

Hi Glen Can you just use RMSD with different sets of atoms in the align and displace weights (two

12/15/25

12/11/25

Uneffective bias for Umbrella Sampling, for studying aggregation

Dear PLUMED developers and users, I hope that all of you are doing well. I am facing some issues

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Uneffective bias for Umbrella Sampling, for studying aggregation

Dear PLUMED developers and users, I hope that all of you are doing well. I am facing some issues

12/11/25

12/11/25

Hi all, I would like to apply a custom potential (piecewise linear in z) to specific atoms, not just

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Hi all, I would like to apply a custom potential (piecewise linear in z) to specific atoms, not just

12/11/25

jerryt...@gmail.com, Omar Valsson4

12/10/25

Plumed Driver error message "Error converting i"

Hi Omar, Thank you. It was the xyz format. I included the --box flag and everything worked out.

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Plumed Driver error message "Error converting i"

Hi Omar, Thank you. It was the xyz format. I included the --box flag and everything worked out.

12/10/25

12/8/25

How to choose sigma when the fluctuation range of the CV in the reactant region is very different from that in the product region

Hi everyone, I'm using metadynamics in PLUMED to study a simple gas-phase association reaction

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How to choose sigma when the fluctuation range of the CV in the reactant region is very different from that in the product region

Hi everyone, I'm using metadynamics in PLUMED to study a simple gas-phase association reaction

12/8/25

Gourav Chakraborty, Michele Invernizzi2

11/29/25

PLUMED restart error

Hi, It seems that the last line in the kernels file is truncated (it has only 3 numbers instead of 5)

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PLUMED restart error

Hi, It seems that the last line in the kernels file is truncated (it has only 3 numbers instead of 5)

11/29/25

Domenico Marson2

11/16/25

Difference in reweighting between plumed 2.9.3 and 2.10.0

I noticed that it seems that the plumed 2.10 version simply ignores the LOGWEIGHTS=weights keyword,

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Difference in reweighting between plumed 2.9.3 and 2.10.0

I noticed that it seems that the plumed 2.10 version simply ignores the LOGWEIGHTS=weights keyword,

11/16/25

10/31/25

Question about MIN keyword in ALPHARMSD (PLUMED 2.9.3 vs 2.10.x)

Hi, I'm trying to use the collective variable ALPHARMSD with the MIN option, and I'm getting

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Question about MIN keyword in ALPHARMSD (PLUMED 2.9.3 vs 2.10.x)

Hi, I'm trying to use the collective variable ALPHARMSD with the MIN option, and I'm getting

10/31/25

Aritra Banerjee

10/31/25

Dynamic atom selection

Hi all, I wanted to restraint the atoms inside a box of z dimensions 2-4 nm in a system. So when I

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Dynamic atom selection

Hi all, I wanted to restraint the atoms inside a box of z dimensions 2-4 nm in a system. So when I

10/31/25

Sriram Vignesh AK, Qinghua Liao2

10/23/25

Metadynamics i-pi+PLUMED

Hello, For your metadynamcis, the pace is too small, the height is too huge, even BIASFACTOR might be

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Metadynamics i-pi+PLUMED

Hello, For your metadynamcis, the pace is too small, the height is too huge, even BIASFACTOR might be

10/23/25

10/21/25

Issue Regarding q6 module

Hi everyone, I had 2 queries using the Q6 module in 2.10 and 2.8 versions 1. I had been using the Q6

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Issue Regarding q6 module

Hi everyone, I had 2 queries using the Q6 module in 2.10 and 2.8 versions 1. I had been using the Q6

10/21/25

Blue Schmitz, … Giovanni Bussi4

10/15/25

Partial tempering changes charge of protein?

You have a molecule with charge -1, in a solution with 739 Na+ and 738 Cl-. You scale the charges of

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Partial tempering changes charge of protein?

You have a molecule with charge -1, in a solution with 739 Na+ and 738 Cl-. You scale the charges of

10/15/25

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