MBX-users

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Welcome to the MBX users group! Feel free to post and ask about any issue or question of the MBX software package. Please see if your question has already been answered in previous posts.

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Shuai Chen, … Henry Agnew8

10:57 AM

Disappeared .so file

By the way, I would like to ask if the python interface has some relevant documentations? It seems

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Disappeared .so file

By the way, I would like to ask if the python interface has some relevant documentations? It seems

10:57 AM

M. X. L (M. X.)

10:57 AM

Should config.nrg should no longer follow the initial configuration if the system changes during MD?

Dear MBX users and developers, I'm using MB-pol with i-Pi software for PIMD simulations. My

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Should config.nrg should no longer follow the initial configuration if the system changes during MD?

Dear MBX users and developers, I'm using MB-pol with i-Pi software for PIMD simulations. My

10:57 AM

Kory, Philip Zhu4

Apr 23

Pair Correlation function g(r) in lammps

Hey, I wanted to ask again how I can calculate the pair correlation function with MB-Pol for smaller

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Pair Correlation function g(r) in lammps

Hey, I wanted to ask again how I can calculate the pair correlation function with MB-Pol for smaller

Apr 23

Ke Xu (徐克), … Henry Agnew14

Apr 22

Get the water virial from C++ program

The newest version of MBX v1.1 has been released publicly, and contains the fixes described

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Get the water virial from C++ program

The newest version of MBX v1.1 has been released publicly, and contains the fixes described

Apr 22

Ethan Bull-vulpe

Apr 22

Announcement: MBX 1.1 Released!

Hello MBX-users, MBX 1.1 has been released on GitHub. See here: https://github.com/paesanilab/MBX/

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Announcement: MBX 1.1 Released!

Hello MBX-users, MBX 1.1 has been released on GitHub. See here: https://github.com/paesanilab/MBX/

Apr 22

Ke Xu (徐克), … Xuanyu Zhu9

Apr 18

Why is the force obtained by MBX in lmp inconsistent with the force in C++?

> “After checking, the force in the LMP you output is exactly the same as the force in C++, even

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Why is the force obtained by MBX in lmp inconsistent with the force in C++?

> “After checking, the force in the LMP you output is exactly the same as the force in C++, even

Apr 18

M. X. L (M. X.), Henry Agnew3

Apr 14

The inet socket on the HPC system with i-PI

Great job on solving this problem and thank you for letting us know about the successful outcome. As

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The inet socket on the HPC system with i-PI

Great job on solving this problem and thank you for letting us know about the successful outcome. As

Apr 14

Zailing Song, Henry Agnew2

Apr 14

fix mbx print/dipoles in lammps

Dear Song, Were you able to fix this issue since you posted, or are you still encountering this error

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fix mbx print/dipoles in lammps

Dear Song, Were you able to fix this issue since you posted, or are you still encountering this error

Apr 14

M. X. L (M. X.), Richa Rashmi3

Mar 30

Dipole data with i-PI to analyze IR spectra

Thank you! It's very hepful for me!!!! 在2024年3月29日星期五 UTC+8 03:16:01<Richa Rashmi> 写道： Dear

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Dipole data with i-PI to analyze IR spectra

Thank you! It's very hepful for me!!!! 在2024年3月29日星期五 UTC+8 03:16:01<Richa Rashmi> 写道： Dear

Mar 30

Asylbek Zhanserkeev, Francesco Paesani2

Mar 23

Dipole extraction and external fields via LAMMPS interface

Dear Asylbek, Thank you for your interest in MBX, and our apologies for the delay in getting back to

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Dipole extraction and external fields via LAMMPS interface

Dear Asylbek, Thank you for your interest in MBX, and our apologies for the delay in getting back to

Mar 23

Nagaprasad, … Francesco Paesani12

Feb 29

Energy is not conserved

Hi Daniel, Thank you, this is reassuring. Nevertheless, a cutoff smaller than 9.0 A implies that some

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Energy is not conserved

Hi Daniel, Thank you, this is reassuring. Nevertheless, a cutoff smaller than 9.0 A implies that some

Feb 29

Wenjie LIU, … Henry Agnew11

Feb 25

Concerning the setting of fix mbx in lammps

Dear Henry, I am glad too that with your selfless help we solve such very strange errors. Though it

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Concerning the setting of fix mbx in lammps

Dear Henry, I am glad too that with your selfless help we solve such very strange errors. Though it

Feb 25

Bernd Hartke, … Xuanyu Zhu3

Feb 14

correction: ``` Note that this is under the branch mbpol23 (while the master branch does not contain

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correction: ``` Note that this is under the branch mbpol23 (while the master branch does not contain

Feb 14

Louis Lehmann, Francesco Paesani4

Feb 13

ion-ion interactions

Hi Louis, We don't recommend doing this because we are seeing interesting many-body effects (

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ion-ion interactions

Hi Louis, We don't recommend doing this because we are seeing interesting many-body effects (

Feb 13

Joe Heindel, Ethan Bull-vulpe2

Feb 2

Getting i-TTM Energies from MBX

Hello Joe, You should be able to use the ion-water TTM potentials by doing the following: 1) During

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Getting i-TTM Energies from MBX

Hello Joe, You should be able to use the ion-water TTM potentials by doing the following: 1) During

Feb 2

Nagaprasad, Richa Rashmi7

Jan 31

having problem with test runs with i-pi interface

Dear Richa, Thank you so much for your efforts. On Wednesday, January 31, 2024 at 4:18:50 AM UTC+2

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having problem with test runs with i-pi interface

Dear Richa, Thank you so much for your efforts. On Wednesday, January 31, 2024 at 4:18:50 AM UTC+2

Jan 31

Wenjie LIU, … Yevhen Horbatenko16

Jan 22

Error encountered when install the MBX with mpi enabled

Dear Developers: This evening I added string -ldl in the Makefile.mpi_mbx at the following position:

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Error encountered when install the MBX with mpi enabled

Dear Developers: This evening I added string -ldl in the Makefile.mpi_mbx at the following position:

Jan 22

Francesco Guidarelli Mattioli, Francesco Paesani2

Jan 21

MBPol Potential LAMMPS GPU

Hi Francesco, MB-pol is not yet available on GPUs. A general GPU implementation for data-driven many-

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MBPol Potential LAMMPS GPU

Hi Francesco, MB-pol is not yet available on GPUs. A general GPU implementation for data-driven many-

Jan 21

Daniel Count, … Ethan Bull-vulpe7

12/16/23

meaning of "grid_density_elec" etc

Hi guys, thanks as a lot for the sweeping clarification. I am already looking forward to the next MBX

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meaning of "grid_density_elec" etc

Hi guys, thanks as a lot for the sweeping clarification. I am already looking forward to the next MBX

12/16/23

Ji Woong Yu, … Ethan Bull-vulpe5

12/10/23

about the box param in JSON

Dear Ethan Bull-Vulpe, I appreciate your help with a nice and clear answer. Thanks and Best Regards,

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about the box param in JSON

Dear Ethan Bull-Vulpe, I appreciate your help with a nice and clear answer. Thanks and Best Regards,

12/10/23

Holo Santis, Francesco Paesani4

11/10/23

output polarizability of water and MB-SCAN

Dear Santis, Thank you for your patience. Our latest paper on ion hydration using the MB-SCAN and MB-

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output polarizability of water and MB-SCAN

Dear Santis, Thank you for your patience. Our latest paper on ion hydration using the MB-SCAN and MB-

11/10/23

Bowen Han, Francesco Paesani3

10/4/23

Run i-Pi with MBX for heavy water

Hi Francesco, thank you very much for your help. I found that there is a way to set the mass of the

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Run i-Pi with MBX for heavy water

Hi Francesco, thank you very much for your help. I found that there is a way to set the mass of the

10/4/23

Bowen Han, Henry Agnew4

9/26/23

Sockets on i-Pi Driver

Hi Henry, I think I enabled the inet with some modification of the code (correctly?). I tried to use

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Sockets on i-Pi Driver

Hi Henry, I think I enabled the inet with some modification of the code (correctly?). I tried to use

9/26/23

Philip Zhu, Bowen Han2

9/26/23

Re: How to control the parallel running with i-Pi

Thanks! "export OMP_NUM_THREADS=4" works for me. On Monday, September 25, 2023 at 7:25:25

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Re: How to control the parallel running with i-Pi

Thanks! "export OMP_NUM_THREADS=4" works for me. On Monday, September 25, 2023 at 7:25:25

9/26/23

Ola Starkolis, Philip Zhu2

9/20/23

Inconsistent number of atoms in /../fix_mbx.cpp

The error of "Inconsistent number of atoms" usually indicates that the simulation has run

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Inconsistent number of atoms in /../fix_mbx.cpp

The error of "Inconsistent number of atoms" usually indicates that the simulation has run

9/20/23

qian gao, … Richa Rashmi8

8/21/23

virial for python plugin

Hello Richa, Thank you very much for your help! ! ! I will have a try. Best wishes, Qian 在2023年8月18日

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virial for python plugin

Hello Richa, Thank you very much for your help! ! ! I will have a try. Best wishes, Qian 在2023年8月18日

8/21/23

qian gao, … Richa Rashmi5

6/23/23

MD simulation terminates unexpectedly

Hello Richa, Thank you very much for your help ! ! ! I changed the initial coordinates and It works.

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MD simulation terminates unexpectedly

Hello Richa, Thank you very much for your help ! ! ! I changed the initial coordinates and It works.

6/23/23

qian gao, Ethan Bull-vulpe3

6/21/23

when compile, configure: error: fftw3 cannot be linked

Thanks a lot, Ethan. I found my problem is that the single-thread version installed is single

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when compile, configure: error: fftw3 cannot be linked

Thanks a lot, Ethan. I found my problem is that the single-thread version installed is single

6/21/23

Md Sharif Khan, Francesco Paesani5

5/19/23

FEP calculation in LAMMPS using MBX pair style

Hi Khan, I think that you have to try. MBX already defines a new pair style and modifies pair_*.cpp

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FEP calculation in LAMMPS using MBX pair style

Hi Khan, I think that you have to try. MBX already defines a new pair style and modifies pair_*.cpp

5/19/23

Md Sharif Khan, … Marc Riera7

4/27/23

Problem making MBX perallal

Hello Ethan and Marc, A fresh installation passed all the tests. However, integrating with LAMMPS is

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Problem making MBX perallal

Hello Ethan and Marc, A fresh installation passed all the tests. However, integrating with LAMMPS is

4/27/23

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