fhh2626 / bfee2 Goto Github PK

colvars: Error: no valid components were provided for this collective variable.
FATAL ERROR: Error in the collective variables module (see above for details)
[Partition 0][Node 0] End of program

Dear,

I am experiencing an error, which I think is simple to fix. What happens is that when you balance your system independently, and use the reset files to prepare the data for the free energy calculation, the program over-estimates the values ​​of the center and size vectors of the box, this it results in "the box is too small" errors, I think they could add an option to be able to pass the xsc file to it so that it can read it directly from there. I have experienced this several times, although with a manual correction everything runs fine, but since there are many files where it has to be corrected, it becomes tedious.

What is the distinction between the 'FEP' and 'BAR' estimation methods used in post-treatment alchemical analysis?
Why are there two different calculation method provided, and which one is more effective in prediction?
Also, which of the two methods, 'FEP' or 'BAR', is equivalent to ParseFEP's BAR provided in VMD?"

Hi, i'm getting following error in step 007:

REINITIALIZING VELOCITIES AT STEP 500 TO 310 KELVIN.
TCL: Running for 5000000 steps
colvars: Too many iterations in routine jacobi.
colvars: This is usually the result of an ill-defined set of atoms for rotational alignment (RMSD, rotateReference, etc).
FATAL ERROR: Error in the collective variables module (see above for details)
FATAL ERROR: Error in the collective variables module (see above for details)
colvars: Too many iterations in routine jacobi.
colvars: This is usually the result of an ill-defined set of atoms for rotational alignment (RMSD, rotateReference, etc).
colvars: Too many iterations in routine jacobi.
colvars: This is usually the result of an ill-defined set of atoms for rotational alignment (RMSD, rotateReference, etc).
FATAL ERROR: Error in the collective variables module (see above for details)
FATAL ERROR: Error in the collective variables module (see above for details)
[Partition 0][Node 0] End of program
FATAL ERROR: Error in the collective variables module (see above for details)
colvars: Too many iterations in routine jacobi.
colvars: This is usually the result of an ill-defined set of atoms for rotational alignment (RMSD, rotateReference, etc).
FATAL ERROR: Error in the collective variables module (see above for details)
colvars: Too many iterations in routine jacobi.
colvars: This is usually the result of an ill-defined set of atoms for rotational alignment (RMSD, rotateReference, etc).
FATAL ERROR: Error in the collective variables module (see above for details)
colvars: Too many iterations in routine jacobi.
colvars: This is usually the result of an ill-defined set of atoms for rotational alignment (RMSD, rotateReference, etc).
FATAL ERROR: Error in the collective variables module (see above for details)
colvars: Too many iterations in routine jacobi.
colvars: This is usually the result of an ill-defined set of atoms for rotational alignment (RMSD, rotateReference, etc).
FATAL ERROR: Error in the collective variables module (see above for details)
FATAL ERROR: Error in the collective variables module (see above for details)
FATAL ERROR: Error in the collective variables module (see above for details)
FATAL ERROR: Error in the collective variables module (see above for details)
FATAL ERROR: Error in the collective variables module (see above for details)
FATAL ERROR: Error in the collective variables module (see above for details)

Hi,
The BFEE2Gui.py Generate Inputs button is giving a window error whatever directory you select: "Selection correspond to nothing! Check your selection again!"
Please, could you give us some guide to fix it? Thank you very much in advance for your reply.

• Install through pip on windows
• Install through conda on windows
• Install through pip on Ubuntu
• Install through conda on Ubuntu
• Install through pip on MacOS
• Install through conda on MacOS
• Install through pip on OpenSUSE
• Install through conda on OpenSUSE
• Generate CHARMM files of a globular protein on Windows
• Generate CHARMM files of a membrane protein on Windows
• Generate Amber files of a globular protein on Windows
• Generate Gromacs files of a globular protein on Windows
• Post-treat alchemical files on Windows
• Post-treat geometrical files on Windows
• Merge files on Windows
• Quick-plot files on Windows
• Plot time evolution of RMSD on Windows
• Help on windows
• Generate CHARMM files of a globular protein on Ubuntu
• Generate CHARMM files of a membrane protein on Ubuntu
• Generate Amber files of a globular protein on Ubuntu
• Generate Gromacs files of a globular protein on Ubuntu
• Post-treat alchemical files on Ubuntu
• Post-treat geometrical files on Ubuntu
• Merge files on Ubuntu
• Quick-plot files on Ubuntu
• Plot time evolution of RMSD on Ubuntu
• Help on Ubuntu
• Generate CHARMM files of a globular protein on MacOS
• Generate CHARMM files of a membrane protein on MacOS
• Generate Amber files of a globular protein on MacOS
• Generate Gromacs files of a globular protein on MacOS
• Post-treat alchemical files on MacOS
• Post-treat geometrical files on MacOS
• Merge files on MacOS
• Quick-plot files on MacOS
• Plot time evolution of RMSD on MacOS
• Help on MacOS
• Generate CHARMM files of a globular protein on OpenSUSE
• Generate CHARMM files of a membrane protein on OpenSUSE
• Generate Amber files of a globular protein on OpenSUSE
• Generate Gromacs files of a globular protein on OpenSUSE
• Post-treat alchemical files on OpenSUSE
• Post-treat geometrical files on OpenSUSE
• Merge files on OpenSUSE
• Quick-plot files on OpenSUSE
• Plot time evolution of RMSD on OpenSUSE
• Help on OpenSUSE

I am using the alchemical route for NAMD. as suggested in the readme file I run the 000.3_updateCenters.py in the 000_eq folder after completion of 000.1_eq.conf but the first line of the message shows that the "colvars2.in does not exist!" . Rest all files are updated

The files I have in the 000_eq folder are colvars.in and colvars_ligandOnly.in

FATAL ERROR: redistrib lone pair forces: no Lphost exists for LP 15891

My ligand have lone pairs. I set the "lonepairs on" in the .conf file and it run smooth however sometimes it give the above error. But when I restart the calculations from start it disappears.

Hi, I got a question about the statement:
"To calculate the binding free energy:

1.1 run 000_eq/000.1_eq.conf
1.2. (optionally) run 000_eq/000.2_updateCenters.py
(If this is done, then there is usually no need to change restraining centers
after steps 3.x.)"

I am a litte confused by the word "after". What does "after steps 3.x." actually mean?
Do I need to update the centers again with the position of the respective PMF minima when using the 000_eq/000.2_updateCenters.py pyscript or not?

https://github.com/fhh2626/BFEE2/blob/92352ae884d4499f27885d013410852370495f0f/BFEE2/templates_readme/Readme_NAMD_Geometrical.txt

• Option to generate parallel runs in the geometrical route
• Documentation of python API
• Generate files for extending simulations in the geometrical route
• Make Help option work
• Make Add and Clear button Grey when using Amber FF
• When cancel the directory selection, BFEE2 should do nothing
• Generate readme file in the BFEE dir
• Rename .conf files
• Do not overwrite ./BFEE folder, raise an Error instead

HelloProfessor,
What I am trying to do is separate a small DNA fragment from the binding pocket of a protein and plot the free energy path. Should I use BFEE for this purpose, considering a DNA molecule has sidechain atoms and is more flexible than a small ligand?

Thank you so much
Yasir

Thank you for your contributions. The article(doi: 10.1038/s41596-021-00676-1) says it provides example data，but I couldn't find any supplementary materials. May I ask if you can provide it? This example data is important for me as a beginner to learn。

FATAL ERROR: CUDA error in ComputeBondedCUDA:: forceDoneCheck after polling 13 times over 0.001407 s on Pe 4 (iks device 0 pci 0:1:0): an illegal memory access was encountered

I have proviously cauculated the binding free energy using BFEE2 tool but in another calculation which has lone pairs the above error is coming.

Hi
I tried to use the GUI with my Ligand + Protein setup with GROMACS:

000_eq worked fine and produced output directly inside 000_eq NOT inside 000_eq/output
and the suffix .out was missing

002_euler_theta I could not generate its tpr file until I copied the output from 000_eq/000_eq.* to 000_eq/output and renamed the to have the .out prefix

Though if I am not mistaken either output redirection/renaming (hint) is missing or just the path at these lines are wrong.

Cheers
René

While working on Post Treatment, Getting the following error

AssertionError
Traceback (most recent call last):
File "/home/singam2/anaconda3.7/envs/bfee/lib/python3.9/site-packages/BFEE2/gui.py", line 1369, in f
self._showGeometricResults(unit)
File "/home/singam2/anaconda3.7/envs/bfee/lib/python3.9/site-packages/BFEE2/gui.py", line 1250, in _showGeometricResults
result = pTreat.geometricBindingFreeEnergy(pmfs, parameters)
File "/home/singam2/anaconda3.7/envs/bfee/lib/python3.9/site-packages/BFEE2/postTreatment.py", line 229, in geometricBindingFreeEnergy
contributions[6] = self._geometricCalculateSI(
File "/home/singam2/anaconda3.7/envs/bfee/lib/python3.9/site-packages/BFEE2/postTreatment.py", line 164, in _geometricCalculateSI
assert(rStar <= pmf[0][-1])
AssertionError

what would be the reason for this?

2021-07-13 16:03:31,250 [BFEEGromacs][007][INFO]:Generating simulation files for D://BFEE/007_r...
2021-07-13 16:03:31,250 [BFEEGromacs][007][INFO]:Making directory D:\miniconda3\Scripts/D:/BFEE/007_r...
[WinError 123]

I suspect this is due to the use of posixpath in BFEEGromacs, which should always be replaced by os.path @HanatoK

@HanatoK
I got the error when distributing BFEE 2,4.1:

python setup.py sdist bdist_wheel
twine upload dist/*

Uploading BFEE2-2.4.1-py3-none-any.whl
100% ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 246.6/246.6 kB • 00:01 • 230.2 kB/s
WARNING  Error during upload. Retry with the --verbose option for more details.
ERROR    HTTPError: 400 Bad Request from https://upload.pypi.org/legacy/
         Wheel 'BFEE2-2.4.1-py3-none-any.whl' does not contain the required METADATA file:
         bfee2-2.4.1.dist-info/METADATA

Is there something new for setuptools that we are missing?

I downloaded the BFEE VMD plugin and was looking to perform binding calculations for a protein-protein system. I noticed that it does not let me select the protein:protein option and only allows for the selection of the protein:ligand option. What is the reason for this?
What would be the best way to go about performing these calculations for a protein-protein system?

Hello @fhh2626 @HanatoK

Should the inputs for the complex already be solvated for the pre-treatment or does BFEE2 do this for us?

How do I know which parameter files I need to include from CHARMM-GUI in BFEE2 to generate the correct files? I keep receiving errors seemingly no matter which parameter files I include, unknown parameters or bad format.

Hello,
In your nature protocol paper did you use NAMD 3.0 GPU version to run the simulations? Did you use "CUDASOAintegrate on" in the input file which is required for high performance? The reason I ask is because in the SI it looks like you used 32 CPU cores and 2 GTX 2080Ti. However, when using "CUDASOAintegrate on" with NAMD 3.0 I get the following:

REPLICA 1 FATAL ERROR: CUDASOA integration is incompatible with the following options:
minimization; pressure profiling; Berendsen pressure;
multigrator; Lowe-Andersen; fixed atoms; GBIS; LCPO;
zero momentum; TCL forces; Colvars;
temperature coupling, rescaling, or reassignment;
water models other than TIP3; lonepairs or Drude.

How was your NAMD 3.0 able to run using multiple GPUs with colvars when it says it is not yet supported? Or do I have to compile with the NAMD git version of Colvars to get that functionality? Or did you not run with "CUDASOAintegrate on" ?

I'm trying to run geometric route, and it recommends doing a layering, but I don't know how to do this, is there any basis for this?

Geo.

After alchemical analysis, when we perform Post-treatment, we provide .feout and .log files for calculating the binding energy, what values it takes from the .log file for calculating energy.

I suggest we hard-code the file names as many as possible to avoid potential issues in making files

Hi,
After clicking the Generate Inputs button in the BFEE2Gui Pre-treatment tab, an error window is showed containing the following text:
"Unknown error! The error message is: The true value of an array with more than one element is ambiguous. Use a.any() or a.all()"

Please, could you point us to the meaning of such an error message in order we can deal with it? Thank you very much in advance for your reply.

Dear Professor Fu：

Thank you very much for your report, which has taught me a lot. While attempting to use BFEE2 and performing simulations with Gromacs, I encountered an error during the final post-processing step: ‘r_star cannot be larger than r_max of step 7!’.

However, when I set r_star to a sufficiently small value, I received another error: ‘Unknown error! The error message is: math range error’.

I am unsure how to proceed with resolving these issues, so I am seeking your guidance. Thank you very much for your advice!

Attached is the pmf file for this calculation.
czar_pmf_file.zip
Once again, thank you for your work！

Hi,
Can BFEE2 be used for membrane proteins?

Hi,
In your Nature Protocols procedure, OPLS was listed as an available FF. However, I only see options for CHARMM and AMBER when running BFEE2GUI. Can top_ and par_ files from the OPLS-AA site be added in the Force Field section? CHARMM does not support the molecule that I am parameterizing.

I have tried to create simulation files using both BFEE and BFEE2 and no matter what whenever I run simulation on step 002_euler_theta I get the same error:

ERROR: Constraint failure in RATTLE algorithm for atom 2572!
ERROR: Constraint failure; simulation has become unstable.

I have tried everything suggested online. Including changing the timestep, increasing minimization to get rid of unfavorable contacts, increasing margin, etc. However, nothing has worked.

Are there any suggestions?

@fhh2626 @HanatoK
Thank you!

• increase force constants used in pinning down the protein
• add a script, letting user to use the equilibrated structure as the reference
• correct periodicity of polarPhi

Dar,

I'm try use it as an python module to use it into jupyter notebook or scripts, please can given me any example to do it?

Geo.

I failed to install BFEE2 by conda with the following command: conda install -c conda-forge bfee2 .

(base) PS C:\Users\tangw> conda install -c conda-forge bfee2
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

On page 1126-1127 chapter 10 of your journal you change the center to -2:
harmonic {
colvars eulerTheta
forceConstant 0.1
centers -2.0
}

what I want to ask here is whether the value centers -2 applies to all simulated systems?

Hello,

Is there any tutorial to learn how to use BFEE2?

In a previous issue (#56) protein-protein calculation is not implemented. Is it yet? Should I use the approach you suggested in the issue to compute the binding free energy of a protein complex?

Thanks in advance.

we should use Parrinello-Rahman barostat in Gromacs, as Berendsen barostat is generally thought to be bad

Dear all,

I'm experience the following mistakes:

1. I have prepared my system using charmm-gui (protein-ligand). when I run the equilibration step the target temperature is in average 309 K (my target is 310.15) which do sense. But when I run the production the average temperature is about 307 K, Which is the motive to it? . Note: Langevin thermostats is used.

2. When I change from langevin to veolicity rescaling (busi) thermostat my simulation keep about 310 K, but I want to know if is right to using the second one thermostat.

FATAL ERROR: Periodic cell has become too small for original patch grid!
There are probably many margin violations already reported.
Possible solutions are to restart from a recent checkpoint, increase margin, or disable useFlexibleCell for liquid simulation.

I have increased the margin, disable useFlexibleCell still it is showing the same error.

Is there a step-by-step tutorial for installing the BFEE2 VMD Plugin?

I tried to install BFEE2 using conda on my Windows machine, but I am running into an issue. I get an error that the module Pyside2 cannot be found:

(base) C:\Users\Christos>python3 C:\Users\Christos\anaconda3\Scripts\BFEE2Gui.py
Traceback (most recent call last):
  File "C:\Users\Christos\anaconda3\Scripts\BFEE2Gui.py", line 43, in <module>
    from PySide2.QtWidgets import QApplication
ModuleNotFoundError: No module named 'PySide2'

However, during the installation process, I can see that pyside2 was installed:

The following NEW packages will be INSTALLED:

  appdirs            conda-forge/noarch::appdirs-1.4.4-pyh9f0ad1d_0
  bfee2              conda-forge/noarch::bfee2-2.3.0-pyhd8ed1ab_0
  biopython          conda-forge/win-64::biopython-1.79-py38h294d835_1
  brotli             conda-forge/win-64::brotli-1.0.9-h8ffe710_7
  brotli-bin         conda-forge/win-64::brotli-bin-1.0.9-h8ffe710_7
  cftime             conda-forge/win-64::cftime-1.6.0-py38hbdcd294_1
  curl               pkgs/main/win-64::curl-7.82.0-h2bbff1b_0
  cycler             conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
  fonttools          conda-forge/win-64::fonttools-4.33.3-py38h294d835_0
  griddataformats    conda-forge/noarch::griddataformats-0.7.0-pyhd8ed1ab_0
  gsd                conda-forge/win-64::gsd-2.5.2-py38hbdcd294_0
  hdf4               conda-forge/win-64::hdf4-4.2.15-h0e5069d_3
  hdf5               conda-forge/win-64::hdf5-1.12.1-nompi_h2a0e4a3_100
  joblib             conda-forge/noarch::joblib-1.1.0-pyhd8ed1ab_0
  kiwisolver         conda-forge/win-64::kiwisolver-1.4.2-py38hbd9d945_1
  libbrotlicommon    conda-forge/win-64::libbrotlicommon-1.0.9-h8ffe710_7
  libbrotlidec       conda-forge/win-64::libbrotlidec-1.0.9-h8ffe710_7
  libbrotlienc       conda-forge/win-64::libbrotlienc-1.0.9-h8ffe710_7
  libclang           conda-forge/win-64::libclang-11.1.0-default_h5c34c98_1
  libcurl            pkgs/main/win-64::libcurl-7.82.0-h86230a5_0
  libnetcdf          conda-forge/win-64::libnetcdf-4.8.1-nompi_h1cc8e9d_101
  libssh2            conda-forge/win-64::libssh2-1.10.0-h680486a_2
  libxslt            conda-forge/win-64::libxslt-1.1.33-h65864e5_2
  libzip             conda-forge/win-64::libzip-1.8.0-hfed4ece_1
  m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6
  m2w64-gcc-libs     conda-forge/win-64::m2w64-gcc-libs-5.3.0-7
  m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7
  m2w64-gmp          conda-forge/win-64::m2w64-gmp-6.1.0-2
  m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2
  matplotlib-base    conda-forge/win-64::matplotlib-base-3.5.1-py38h1f000d6_0
  mdanalysis         conda-forge/win-64::mdanalysis-2.1.0-py38h885f38d_1
  mmtf-python        conda-forge/noarch::mmtf-python-1.1.2-py_0
  mrcfile            conda-forge/noarch::mrcfile-1.3.0-pyh44b312d_0
  msgpack-python     conda-forge/win-64::msgpack-python-1.0.3-py38hbd9d945_1
  msys2-conda-epoch  conda-forge/win-64::msys2-conda-epoch-20160418-1
  munkres            conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
  netcdf4            conda-forge/win-64::netcdf4-1.5.8-nompi_py38h0500770_101
  networkx           conda-forge/noarch::networkx-2.8-pyhd8ed1ab_0
  pandas             conda-forge/win-64::pandas-1.4.2-py38hcc40339_1
  parmed             conda-forge/win-64::parmed-3.4.3-py38heb73c8a_2
  patsy              conda-forge/noarch::patsy-0.5.2-pyhd8ed1ab_0
  pyqt-impl          conda-forge/win-64::pyqt-impl-5.12.3-py38h885f38d_8
  pyqt5-sip          conda-forge/win-64::pyqt5-sip-4.19.18-py38h885f38d_8
  pyqtchart          conda-forge/win-64::pyqtchart-5.12-py38h885f38d_8
  pyqtwebengine      conda-forge/win-64::pyqtwebengine-5.12.1-py38h885f38d_8
  pyside2            conda-forge/win-64::pyside2-5.13.2-py38hadd4fab_7
  scikit-learn       conda-forge/win-64::scikit-learn-1.0.2-py38hb60ee80_0
  scipy              conda-forge/win-64::scipy-1.8.0-py38ha1292f7_1
  seaborn            conda-forge/noarch::seaborn-0.11.2-hd8ed1ab_0
  seaborn-base       conda-forge/noarch::seaborn-base-0.11.2-pyhd8ed1ab_0
  statsmodels        conda-forge/win-64::statsmodels-0.13.2-py38h6f4d8f0_0
  threadpoolctl      conda-forge/noarch::threadpoolctl-3.1.0-pyh8a188c0_0
  unicodedata2       conda-forge/win-64::unicodedata2-14.0.0-py38h294d835_1

In any case, I would prefer to be able to use the VMD plugin but I cannot seem to find any information how to install the extension into VMD.

I get the following error when I use gromacs topology and pdb file

2021-06-02 19:52:23,939 [BFEEGromacs][INFO]:Initialization done.
2021-06-02 19:52:23,939 [BFEEGromacs][INFO]:Initialization done.
2021-06-02 19:52:23,939 [BFEEGromacs][INFO]:Setup the atoms group of the protein by selection: protein and not (name H*)
2021-06-02 19:52:23,939 [BFEEGromacs][INFO]:Setup the atoms group of the protein by selection: protein and not (name H*)
2021-06-02 19:52:24,345 [BFEEGromacs][INFO]:Setup the atoms group of the ligand by selection: resname VDY and not (name H*)
2021-06-02 19:52:24,345 [BFEEGromacs][INFO]:Setup the atoms group of the ligand by selection: resname VDY and not (name H*)
2021-06-02 19:52:24,628 [BFEEGromacs][INFO]:Setup the atoms group of the solvent molecule by selection: resname TIP3* or resname SPC*
2021-06-02 19:52:24,628 [BFEEGromacs][INFO]:Setup the atoms group of the solvent molecule by selection: resname TIP3* or resname SPC*
qt.glx: qglx_findConfig: Failed to finding matching FBConfig for QSurfaceFormat(version 2.0, options QFlagsQSurfaceFormat::FormatOption(), depthBufferSize -1, redBufferSize 1, greenBufferSize 1, blueBufferSize 1, alphaBufferSize -1, stencilBufferSize -1, samples -1, swapBehavior QSurfaceFormat::SingleBuffer, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile)
No XVisualInfo for format QSurfaceFormat(version 2.0, options QFlagsQSurfaceFormat::FormatOption(), depthBufferSize -1, redBufferSize 1, greenBufferSize 1, blueBufferSize 1, alphaBufferSize -1, stencilBufferSize -1, samples -1, swapBehavior QSurfaceFormat::SingleBuffer, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile)
Falling back to using screens root_visual.

Can you help me rectify this error?

Dear Dr Fu,
Does BFEE support alchemical calculations of ligands with a nonzero net charge? I read that having a charge perturbation can lead to artifacts which require correction terms. Does BFEE2 consider those by default?

If not, could you please point me to an alternative that would allow me to do such calculations?

Best regards,
Pranav

Hello,

I'm running simulations using your method (BFEE2) and I have a question about the forceconstant value in the free energy calculation function (e.g. geometricRestraintContribution). Is this the force constant defined for each harmonic restraint or is it the scaled value of it (forceconstant is scaled according to the specified width)?

Thank you!

Compatibility:

• generate NAMD geometrical files on Windows
• generate NAMD alchemical files on Windows
• generate Gromacs geometrical files on Windows
• generate NAMD geometrical files on Linux
• generate NAMD alchemical files on Linux
• generate Gromacs geometrical files on Linux
• generate NAMD geometrical files on Mac OS
• generate NAMD alchemical files on Mac OS
• generate Gromacs geometrical files on Mac OS

NAMD geometrical:

• generate correct files when not linked with VMD
• generate correct files when linked with VMD
• generate executable files for stratified windows
• generate executable files for extending simulation
• correctly set pulling direction
• correctly set membrane protein
• correctly set number of parallel runs
• generate correct files when using Amber FF
• correctly set pulling direction when using Amber FF
• correctly set membrane protein when using Amber FF
• correctly set number of parallel runs when using Amber FF
• generate executable files for stratified windows when using Amber FF
• generate executable files for extending simulation when using Amber FF
• not overwrite./BFEE
• raise error and remove ./BFEE when selection is wrong

NAMD alchemical

• generate correct files when not linked with VMD
• generate correct files when linked with VMD
• correctly set stratification windows
• correctly set minimize before sampling
• correctly set membrane protein
• generate correct files when using Amber FF
• correctly set minimize before sampling when using Amber FF
• correctly set membrane protein when using Amber FF
• not overwrite./BFEE
• raise error and remove ./BFEE when selection is wrong

Gromacs geometrical

• generate executable files
• not overwrite./BFEE
• raise error and remove ./BFEE when selection is wrong
• show error message when wrong selections are used for BFEEGromacs

Other issues

• Help option
• Python API option
• raise an error when FF is empty when using the CHARMM files
• let FF selection be gray when using the Amber files
• when cancel selection of dir, BFEE should do nothing
• create correct Readme file for the NAMD geometrical route
• create correct Readme file for the NAMD alchemical route
• create correct Readme file for the Gromacs geometrical route
• corrected filenames for *.conf

Hi, when I tried to simulate after "Generate Inputs" on a no GPU Ubuntu system.
Do you have any suggestions on GPU usage?

Thanks

Hello,

I generated the inputs for an alchemical transformation. During the first equilibration step, I am getting this error for the eulerPhi variable for the complex:

...
colvars: Error parsing expression "atan2(2*(q1*q2+q3*q4), 1-2*(q2*q2+q3*q3)) * 180 / 3.1415926".
FATAL ERROR: Error in the collective variables module: exiting.
...

Any idea about how to solve it? I am new with the colvars module.

Thanks in advance.
Best,
Yasser

Hi,

what is the reason that in
NAMD colvars files hillWeight 0.05 is used
while for GROMACS colvars files hillWeight 0.2092 is used?

Cheers
René

I have encountered interruptions during NAMD alchemical route binding energy calculations due to power failures, causing the job to stop. I am exploring the possibility of utilizing BFEE2 to generate files that enable the resumption of calculations from the point of interruption. Additionally, I am curious if there are specific configurations or adjustments needed in the .conf files within both the Bound and Unbound folders to facilitate the seamless continuation of the job.

Hi, i'm getting following error in step 007:
I'm using NAMD (3.0a6/2.14), and when running 007.1 step of equilibration I'm getting it error:
FATAL ERROR: CudaTileListKernel::buildTileLists, maximum shared memory allocation exceeded. Too many atoms in a patch

I'm trying to learn to run this software. Program 1 looks fine. When running program 2 I encountered the following problem

input files from https://www.nature.com/articles/s41596-021-00676-1#Sec47
41596_2021_676_MOESM3_ESM\Workflow_geometrical\Input\complex.pdb & complex.psf & par_all36m_prot.prm & toppar_water_ions.prm

namd3 002_abf_1.conf > 002_abf_1.conf.log &
[2] 2891
$ FATAL ERROR: Unable to open extended system file.

The file content of 002_abf_1.conf is as follows :
coordinates ../complex.pdb
structure ../complex.psf
paraTypeCharmm on
parameters ../par_all36m_prot.prm
parameters ../toppar_water_ions.prm
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 14.0
bincoordinates ../000_eq/output/eq.coor
binvelocities ../000_eq/output/eq.vel
ExtendedSystem ../000_eq/output/eq.xsc
binaryoutput yes
binaryrestart yes
outputname output/abf_1
dcdUnitCell yes
outputenergies 5000
outputtiming 5000
outputpressure 5000
restartfreq 5000
XSTFreq 5000
dcdFreq 5000
hgroupcutoff 2.8
wrapAll off
wrapWater on
langevin on
langevinDamping 1
langevinTemp 300.0
langevinHydrogen no
langevinpiston on
langevinpistontarget 1.01325
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp 300.0
usegrouppressure yes
PME yes
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridSpacing 1.0
timestep 2.0
fullelectfrequency 2
nonbondedfreq 1
rigidbonds all
rigidtolerance 0.00001
rigiditerations 400
stepspercycle 10
splitpatch hydrogen
margin 2
useflexiblecell no
useConstantRatio no
colvars on
accelMD on
accelMDG on
accelMDdihe on
accelMDOutFreq 1000
accelMDGSigma0D 6.0
accelMDGcMDSteps 500000
accelMDGcMDPrepSteps 100000
accelMDGEquiPrepSteps 100000
accelMDGEquiSteps 500000
for {set stage 0} {$stage < 2} {incr stage} {
if {$stage == 0} {
puts "Probing the GaMD parameters..."
cv configfile colvars_1.in
run norepeat 1000000
} elseif {$stage == 1} {
puts "Starting eABF + GaMD..."
cv reset
cv configfile colvars_1.in.amd
run norepeat 5000000
}
}

The file content of 002_abf_1.log is as follows :
Charm++> No provisioning arguments specified. Running with a single PE.
Use +auto-provision to fully subscribe resources or +p1 to silence this message.
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads (PEs)
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID:
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 hosts (1 sockets x 10 cores x 2 PUs = 20-way SMP)
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: Built with CUDA version 11080
Did not find +devices i,j,k,... argument, using all
Pe 0 physical rank 0 binding to CUDA device 0 on DSb: 'NVIDIA GeForce RTX 4070 Ti' Mem: 12281MB Rev: 8.9 PCI: 0:1:0
Info: NAMD 3.0b7 for Linux-x86_64-multicore-CUDA
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 70000 for multicore-linux-x86_64-gcc
Info: Built Fri May 10 16:01:53 CDT 2024 by dhardy on athine.ks.uiuc.edu
Info: 1 NAMD 3.0b7 Linux-x86_64-multicore-CUDA 1 DSb adsb
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.20704 s
CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification)
Info: 0 MB of memory in use based on /proc/self/stat
Info: Configuration file is 002_abf_1.conf
Info: Working in the current directory /mnt/d/BFEE2/New Folder/BFEE/002_EulerTheta
Probing the GaMD parameters...
TCL: Suspending until startup complete.
Warning: Option "1-4scaling" has been deprecated. Instead use "oneFourScaling".
Info: EXTENDED SYSTEM FILE ../000_eq/output/eq.xsc
FATAL ERROR: Unable to open extended system file.

[Partition 0][Node 0] End of program

Is it a problem with the NAMD version or other reasons and can you tell me how to solve this problem?

Running post-treatment reported a error mentioned above.

Thank you for your contributions. when i Patch Gromacs with Colvars (sh ./colvars-master/update-colvars-code.sh ./gromacs-2020.6)，there is an error：./colvars-master/update-colvars-code.sh: 15: hash: Illegal option -t. May I ask what the reason is. How to solve this problem？