GROMACS wizard - Letal Warning during NPT Equilibration step



  • I'm using GROMACS wizard app, that works well during the PREPARATION, MINIMIZATION and NVT EQUILIBRATION steps.
    The issue comes when I go through the NPT simulation.

    These are the errors wrote in the log file:

    **WARNING 1 [file PEP_1_prepared_minimized_nvt_boxed.top, line 48]:
    The bond in molecule-type Protein_chain_A between atoms 61 OG1 and 62 HG1
    has an estimated oscillational period of 9.0e-03 ps, which is less than 5
    times the time step of 2.0e-03 ps.
    Maybe you forgot to change the constraints mdp option.

    Number of degrees of freedom in T-Coupling group Protein is 773.97
    Number of degrees of freedom in T-Coupling group non-Protein is 80514.03

    NOTE 1 [file C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/MdpFiles/npt.mdp]:
    NVE simulation with an initial temperature of zero: will use a Verlet
    buffer of 10%. Check your energy drift!

    NOTE 2 [file C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/MdpFiles/npt.mdp]:
    You are using a plain Coulomb cut-off, which might produce artifacts.
    You might want to consider using PME electrostatics.

    There were 2 notes

    There was 1 warning


    Program gmx grompp, VERSION 5.1
    Source code file: D:\jenkins\workspace\release\Windows\samson-elements\External\gromacs-5.1\src\gromacs\gmxpreprocess\grompp.c, line: 2116

    Fatal error:
    Too many warnings (1), gmx terminated.
    If you are sure all warnings are harmless, use the -maxwarn option.
    For more information and tips for troubleshooting, please check the GROMACS
    website at http://www.gromacs.org/Documentation/Errors
    -------------------------------------------------------**

    Now, generally when I run GROMACS from without using SAMSON, I can pass that problem by using the -maxwarn option.

    Can I add additional option, -maxwarn i.e., when I'm using GROMACS Wizard on SAMSON?

    THANKS in advance!



  • Hello, could you please try to add it in the Additional parameters section of the Simulate tab? (Under "Saving interval", you should see the "All..." push button.

    0_1575649411930_79f6855f-f816-4954-90e0-7ebba96439d6-image.png



  • Hi,
    I've tried to add -maxwarn 1 but doesn't works.



  • Apparently, there are more warnings or the -maxwarn option did not take effect at all. Does the error log show you the same warning or more? If there is more, could you, please, post the log as you did before. It will be very helpful for us. Meanwhile, in the Additional parameters, you can try increasing the maximum number of warnings, e.g.:

    -maxwarn 10
    

    Thank you!



  • This post is deleted!


  • @carmine
    Great! Thank you for your feedback!



  • I'm so sorry Dmitry,

    I've ran di NVT again, not the NPT.
    I tried again and NPT still doesn't works...

    Here the log file:

    ######################################## NVT Equilibration of PEP_1_prepared_minimized_nvt STARTED ########################################

                    :-) GROMACS - gmx mdrun, VERSION 5.1 (-:
    
                            GROMACS is written by:
     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
    

    Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
    Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
    Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
    Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
    Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
    Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
    Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
    and the project leaders:
    Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

    Copyright (c) 1991-2000, University of Groningen, The Netherlands.
    Copyright (c) 2001-2015, The GROMACS development team at
    Uppsala University, Stockholm University and
    the Royal Institute of Technology, Sweden.
    check out http://www.gromacs.org for more information.

    GROMACS is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License
    as published by the Free Software Foundation; either version 2.1
    of the License, or (at your option) any later version.

    GROMACS: gmx mdrun, VERSION 5.1
    Executable: C:\Users\c.talarico\AppData\Local\OneAngstrom\SAMSON-Data\0.8.5\Scratch\Elements\02407D21-0490-30BA-D20F-2E88DB100FC5\Resource\gromacs\gmx.exe
    Data prefix: C:\Program Files\Gromacs
    Command line:
    gmx mdrun -v -s C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/PEP_1_prepared_minimized_nvt_nvt.tpr -deffnm C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/PEP_1_prepared_minimized_nvt_nvt

    Running on 1 node with total 2 cores, 4 logical cores
    Hardware detected:
    CPU info:
    Vendor: GenuineIntel
    Brand: Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: None

    Compiled SIMD instructions: None, GROMACS could use AVX2_256 on this machine, which is better

    The current CPU can measure timings more accurately than the code in
    gmx was configured to use. This might affect your simulation
    speed as accurate timings are needed for load-balancing.
    Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.

    Reading file C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/PEP_1_prepared_minimized_nvt_nvt.tpr, VERSION 5.1 (single precision)

    Using 1 MPI thread
    Using 4 OpenMP threads

    WARNING: Using the slow plain C kernels. This should
    not happen during routine usage on supported platforms.

    starting mdrun 'Protein'
    50000 steps, 100.0 ps.

    step 0

    step 100, will finish Tue Dec 10 15:38:30
    2019

    step 200, will fini
    sh Tue Dec 10 15:35:33 2019

    step 300, will finish Tue Dec 10 15:37:20 2019

    step 400, will finish Tue Dec 10 15:36:08 2019

    step 500, will finish Tue Dec 10 15:38:45 2019

    step 600, will finish
    Tue Dec 10 15:39:06 2019

    step 700, will finish Tue Dec 10 15:40:33 2019

    step 800, will finish Tue Dec 10 15:39:33 2019

    step 900, will finish Tue Dec 10 15:39:42 2019

    step 1000, will finish Tue Dec 10 15:39:49 2019

    step 1100, will finish Tue Dec 10 15:39:55 2019
    All the tasks has been stopped.
    All the tasks has been stopped.
    :-) GROMACS - gmx grompp, VERSION 5.1 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
    

    Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
    Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
    Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
    Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
    Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
    Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
    Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
    and the project leaders:
    Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

    Copyright (c) 1991-2000, University of Groningen, The Netherlands.
    Copyright (c) 2001-2015, The GROMACS development team at
    Uppsala University, Stockholm University and
    the Royal Institute of Technology, Sweden.
    check out http://www.gromacs.org for more information.

    GROMACS is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License
    as published by the Free Software Foundation; either version 2.1
    of the License, or (at your option) any later version.

    GROMACS: gmx grompp, VERSION 5.1
    Executable: C:\Users\c.talarico\AppData\Local\OneAngstrom\SAMSON-Data\0.8.5\Scratch\Elements\02407D21-0490-30BA-D20F-2E88DB100FC5\Resource\gromacs\gmx.exe
    Data prefix: C:\Program Files\Gromacs
    Command line:
    gmx grompp -f C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/MdpFiles/npt.mdp -c C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/PEP_1_prepared_minimized_nvt_2_boxed.gro -r C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/PEP_1_prepared_minimized_nvt_2_boxed.gro -p C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/PEP_1_prepared_minimized_nvt_2_boxed.top -po C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/PEP_1_prepared_minimized_nvt_2_npt_mdout.mdp -o C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/GeneratedFiles/PEP_1_prepared_minimized_nvt_2_npt.tpr

    Generated 330891 of the 330891 non-bonded parameter combinations
    Generating 1-4 interactions: fudge = 0.5
    Generated 330891 of the 330891 1-4 parameter combinations
    Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
    Excluding 3 bonded neighbours molecule type 'Ion_chain_B'
    Excluding 2 bonded neighbours molecule type 'SOL'
    Cleaning up constraints and constant bonded interactions with virtual sites
    Removing all charge groups because cutoff-scheme=Verlet

    WARNING 1 [file PEP_1_prepared_minimized_nvt_2_boxed.top, line 48]:
    The bond in molecule-type Protein_chain_A between atoms 61 OG1 and 62 HG1
    has an estimated oscillational period of 9.0e-03 ps, which is less than 5
    times the time step of 2.0e-03 ps.
    Maybe you forgot to change the constraints mdp option.

    Number of degrees of freedom in T-Coupling group Protein is 773.97
    Number of degrees of freedom in T-Coupling group non-Protein is 80514.03

    NOTE 1 [file C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/MdpFiles/npt.mdp]:
    NVE simulation with an initial temperature of zero: will use a Verlet
    buffer of 10%. Check your energy drift!

    NOTE 2 [file C:/Users/c.talarico/AppData/Local/OneAngstrom/SAMSON-Data/0.8.5/Scratch/GROMACS/MdpFiles/npt.mdp]:
    You are using a plain Coulomb cut-off, which might produce artifacts.
    You might want to consider using PME electrostatics.

    There were 2 notes

    There was 1 warning


    Program gmx grompp, VERSION 5.1
    Source code file: D:\jenkins\workspace\release\Windows\samson-elements\External\gromacs-5.1\src\gromacs\gmxpreprocess\grompp.c, line: 2116

    Fatal error:
    Too many warnings (1), gmx terminated.
    If you are sure all warnings are harmless, use the -maxwarn option.
    For more information and tips for troubleshooting, please check the GROMACS
    website at http://www.gromacs.org/Documentation/Errors


    Program: gmx grompp, VERSION 5.1
    Source file: D:\jenkins\workspace\release\Windows\samson-elements\External\gromacs-5.1\src\gromacs\utility\fatalerror.cpp (line 265)
    Function: void __cdecl do_exit(bool,bool)

    Feature not implemented:
    Fatal error

    For more information and tips for troubleshooting, please check the GROMACS
    website at http://www.gromacs.org/Documentation/Errors



  • GROMACS stops due to GROMACS warnings. Did you add the -maxwarn option in the additional parameters of this step?

    Note, different steps in the GROMACS Wizard (equilibration, simulation, etc) have their own parameters and you may need to specify additional parameters in each one of them.



  • @DmitriyMarin
    Yes, I'm adding -maxwarn option in the additional parameters of Equilibrate menu' after clicking on Isothermal-isobaric (NPT).



  • @carmine said in GROMACS wizard - Letal Warning during NPT Equilibration step:

    WARNING 1 [file PEP_1_prepared_minimized_nvt_2_boxed.top, line 48]:
    The bond in molecule-type Protein_chain_A between atoms 61 OG1 and 62 HG1
    has an estimated oscillational period of 9.0e-03 ps, which is less than 5
    times the time step of 2.0e-03 ps.
    Maybe you forgot to change the constraints mdp option.

    You may need to solve this GROMACS warning by either modifying the time-step or changing the constraints mdp options.



  • For example, try decreasing the Integration time step to 0,001 ps.



  • Hi @DmitriyMarin,
    now really works!!! The reduction of the time-steps allowed completing the equilibration.
    Thank you again!

    One last question:
    If I would like to change the box shape from cubic to rhombic dodecahedron, where can I add the flag -bt dodecahedron?



  • @carmine Great!

    No, for now, GROMACS Wizard supports only the cubic box type, but we can add other box types in the future releases.

    Could you, please, tell us what else you would like to see in the future releases of the GROMACS Wizard or in SAMSON in general?



  • @DmitriyMarin

    I think that by adding the possibility to choose the box type can be a nice feature, for sure.
    In my opinion, another useful feature may be to highlight, in some way, the options that are added into the Additional parameters form, in order to have more clear the extra modifications.



  • @carmine Thank you very much for your feedback!

    We will add other box types in one of the next updates of the GROMACS Wizard.

    Options provided in the Additional parameters have bigger priority then options specified in the GUI. It is true, it would be nice to highlight them in some way.


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