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PLUMED users

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Munazzah Ansari, Giovanni Bussi2

Aug 14

Replica Exchange Acceptance Issue on Different GPUs

Hello I would suggest trying to take a diff of the log files in the different runs. It is possibile

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Replica Exchange Acceptance Issue on Different GPUs

Hello I would suggest trying to take a diff of the log files in the different runs. It is possibile

Aug 14

Aug 10

On issues about xyz format of plumed driver

Dear all: Sorry to bother again, this is my answer as a mark for my dumb mistake. I have always known

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On issues about xyz format of plumed driver

Dear all: Sorry to bother again, this is my answer as a mark for my dumb mistake. I have always known

Aug 10

John Hymel, Gareth Tribello3

Jul 25

Shared Coordination Number

Gareth, This helps a lot! I was able to get this to work using Plumed-driver (when using the Plumed

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Shared Coordination Number

Gareth, This helps a lot! I was able to get this to work using Plumed-driver (when using the Plumed

Jul 25

Mo, Omar Valsson2

Jul 21

plumed + vasp + lammps not printing values to colvar or hills

Hello, Try to add the FLUSH action to your PLUMED input file: https://www.plumed.org/doc-v2.9/user-

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plumed + vasp + lammps not printing values to colvar or hills

Hello, Try to add the FLUSH action to your PLUMED input file: https://www.plumed.org/doc-v2.9/user-

Jul 21

joan.c...@gmail.com, Giovanni Bussi2

Jul 10

Get element from MD engine

Hi! No it is not. We have no API actually to pass the names from the MD code to PLUMED, so currently

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Get element from MD engine

Hi! No it is not. We have no API actually to pass the names from the MD code to PLUMED, so currently

Jul 10

marcel...@gmail.com, alx.th...@gmail.com4

Jun 28

Deriving initial guess for BARRIER

Hi Marcelo, thank you for the clarification! With this context, why are you not just using CV1: COM

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Deriving initial guess for BARRIER

Hi Marcelo, thank you for the clarification! With this context, why are you not just using CV1: COM

Jun 28

Jun 20

SMAC analysis on Plumed

Dear Plumed Users,, I am trying to do SMAC analysis on my system. When I tried to run the code, I am

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SMAC analysis on Plumed

Dear Plumed Users,, I am trying to do SMAC analysis on my system. When I tried to run the code, I am

Jun 20

joan.c...@gmail.com2

Jun 18

**[SOLVED]** Turns out that trjconv resets the atom numbers so that they start at 1 and are

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**[SOLVED]** Turns out that trjconv resets the atom numbers so that they start at 1 and are

Jun 18

Gourav Chakraborty

Jun 15

Plumed error with PESMD

Hello Everyone, I am trying to perform a test PESMD run with plumed, this was my input script:

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Plumed error with PESMD

Hello Everyone, I am trying to perform a test PESMD run with plumed, this was my input script:

Jun 15

Niklas Doering, Carlo C2

Jun 12

PLUMED support for GROMACS 2025/RTX 50-series GPU issues

GROMACS 2025 natively supports plumed without a patch On Thursday, May 22, 2025 at 9:28:51 AM UTC+2

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PLUMED support for GROMACS 2025/RTX 50-series GPU issues

GROMACS 2025 natively supports plumed without a patch On Thursday, May 22, 2025 at 9:28:51 AM UTC+2

Jun 12

Wei Zhang, … Gourav Chakraborty11

Jun 12

Why FES calculated from meta-eabf is not smooth as that from WT-meta?

Hello Everyone, I tried one particular change in the WT-Meta-eABF code, please tell me if I am wrong

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Why FES calculated from meta-eabf is not smooth as that from WT-meta?

Hello Everyone, I tried one particular change in the WT-Meta-eABF code, please tell me if I am wrong

Jun 12

Gourav Chakraborty, … Istvan Kolossvary12

Jun 11

drr is not recognized during eABF plumed

You have to specify a restart drrstate file in the DRR action and put RESTART at the top of the

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drr is not recognized during eABF plumed

You have to specify a restart drrstate file in the DRR action and put RESTART at the top of the

Jun 11

Jun 9

Re: OPES giving -nan entries with eABF

If you are using Colvars, please post your issue on https://github.com/Colvars/colvars/issues. OPES

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Re: OPES giving -nan entries with eABF

If you are using Colvars, please post your issue on https://github.com/Colvars/colvars/issues. OPES

Jun 9

divyabharathi korlepara

May 30

HREX simulations

Dear Plumed users, I'm running Hamiltonian Replica Exchange (HREX) simulations on a protein

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HREX simulations

Dear Plumed users, I'm running Hamiltonian Replica Exchange (HREX) simulations on a protein

May 30

May 22

mindist as the reaction coordinate in AWH

Hi, I'm running umbrella‐sampling simulations in GROMACS + PLUMED and using the minimum distance

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mindist as the reaction coordinate in AWH

Hi, I'm running umbrella‐sampling simulations in GROMACS + PLUMED and using the minimum distance

May 22

Mandar Kulkarni, rjtp...@gmail.com3

May 9

invalid pointer issue with Gromacs-Plumed

Dear PLUMED developers. We are also facing the same issue (free(): invalid pointer) when trying to

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invalid pointer issue with Gromacs-Plumed

Dear PLUMED developers. We are also facing the same issue (free(): invalid pointer) when trying to

May 9

Apr 18

error information in PCA

Hello, everyone, I just met the following error in the compiled plumed: void PLMD::PlumedMain::

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error information in PCA

Hello, everyone, I just met the following error in the compiled plumed: void PLMD::PlumedMain::

Apr 18

Carlos Henrique

Apr 17

segmentation fault for simulations with ntomp > 1

Dear, I've got segmentation fault error for well-tempered molecular dynamics simulations (62610

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segmentation fault for simulations with ntomp > 1

Dear, I've got segmentation fault error for well-tempered molecular dynamics simulations (62610

Apr 17

Евгений Розанов

Apr 16

Local density CV for bubble nucleation

Dear PLUMED users, I am currently investigating argon bubble nucleation and have chosen to use PLUMED

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Local density CV for bubble nucleation

Dear PLUMED users, I am currently investigating argon bubble nucleation and have chosen to use PLUMED

Apr 16

Apr 15

How to use coordination numbers to run metadynamics based path cv?

Dear all, I am trying to reproduce the metadynamics simulation based on Path CV from 10.1073/pnas.

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How to use coordination numbers to run metadynamics based path cv?

Dear all, I am trying to reproduce the metadynamics simulation based on Path CV from 10.1073/pnas.

Apr 15

jamesm...@gmail.com, Giovanni Bussi6

Apr 10

problems across gromacs versions 2023-2025

Thanks Giovanni, This works fine unfortunately. Best wishes James (base) [jkrieger@fmg49 ~]$ ~/bin/

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problems across gromacs versions 2023-2025

Thanks Giovanni, This works fine unfortunately. Best wishes James (base) [jkrieger@fmg49 ~]$ ~/bin/

Apr 10

Santiago Movilla

Apr 3

Custom Potential

Hello PLUMED community, I want to set the bias potential of an angle so that the system mostly stays

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Custom Potential

Hello PLUMED community, I want to set the bias potential of an angle so that the system mostly stays

Apr 3

Saeed Pourasad, Michele Invernizzi2

Mar 27

Missing PLUMED Modules (like OPES) in Conda LAMMPS Installation

Hi, You could use the conda version for plumed masterclass from 2022, it also supports lammps, see

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Missing PLUMED Modules (like OPES) in Conda LAMMPS Installation

Hi, You could use the conda version for plumed masterclass from 2022, it also supports lammps, see

Mar 27

Mar 26

Two kinds of Metadynamics code writing

Hello, I am trying to apply a metad on my system and my original code is like this: ``` METAD ...

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Two kinds of Metadynamics code writing

Hello, I am trying to apply a metad on my system and my original code is like this: ``` METAD ...

Mar 26

Mar 26

Hi All, We have run an umbrella sampling simulation of a molecule traversing a membrane and are

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Hi All, We have run an umbrella sampling simulation of a molecule traversing a membrane and are

Mar 26

Hang LYU, … Siva Bharadwaj V3

Mar 21

A question about running plumed together with cp2k

I installed cp2k with plumed but when I am giving command it is not taking the plumed it is showing

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A question about running plumed together with cp2k

I installed cp2k with plumed but when I am giving command it is not taking the plumed it is showing

Mar 21

Nomula Raghavendra

Mar 18

Calculating Q6 for nuclei in Vapor

Hello, I want to calculate Q6 of the atoms that formed nuclei from vapor. Since I don't know

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Calculating Q6 for nuclei in Vapor

Hello, I want to calculate Q6 of the atoms that formed nuclei from vapor. Since I don't know

Mar 18

Saeed Pourasad, Gareth Tribello3

Mar 17

Advice on CV for OPES Simulations of Water Clusters

Thanks a lot! On Monday, March 17, 2025 at 4:56:15 PM UTC+9 Gareth Tribello wrote: Hello Saeed I am

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Advice on CV for OPES Simulations of Water Clusters

Thanks a lot! On Monday, March 17, 2025 at 4:56:15 PM UTC+9 Gareth Tribello wrote: Hello Saeed I am

Mar 17

Mar 12

how to save a model as CV?

To all developers and users Following the example section of mlcolvars (https://mlcolvar.readthedocs.

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how to save a model as CV?

To all developers and users Following the example section of mlcolvars (https://mlcolvar.readthedocs.

Mar 12

Hu Li, … Luigi Bonati4

Feb 24

About negative value in Structure Factor calculation, it matters my defense.

Many thanks to Michele and Luigi for your precious comments. Before sampling, I tested on cutoff 4

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About negative value in Structure Factor calculation, it matters my defense.

Many thanks to Michele and Luigi for your precious comments. Before sampling, I tested on cutoff 4

Feb 24

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