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    GROMACS wizard - Letal Warning during NPT Equilibration step

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    • C
      Carmine last edited by

      This post is deleted!
      DmitriyMarin 1 Reply Last reply Reply Quote 0
      • DmitriyMarin
        DmitriyMarin @Carmine last edited by

        @carmine
        Great! Thank you for your feedback!

        Dmitriy,
        The SAMSON Team, https://s-c.io

        1 Reply Last reply Reply Quote 1
        • C
          Carmine last edited by

          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

          1 Reply Last reply Reply Quote 0
          • DmitriyMarin
            DmitriyMarin last edited by

            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.

            Dmitriy,
            The SAMSON Team, https://s-c.io

            1 Reply Last reply Reply Quote 1
            • C
              Carmine last edited by

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

              1 Reply Last reply Reply Quote 0
              • DmitriyMarin
                DmitriyMarin last edited by

                @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.

                Dmitriy,
                The SAMSON Team, https://s-c.io

                1 Reply Last reply Reply Quote 1
                • DmitriyMarin
                  DmitriyMarin last edited by

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

                  Dmitriy,
                  The SAMSON Team, https://s-c.io

                  1 Reply Last reply Reply Quote 1
                  • C
                    Carmine last edited by

                    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?

                    DmitriyMarin 1 Reply Last reply Reply Quote 1
                    • DmitriyMarin
                      DmitriyMarin @Carmine last edited by

                      @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?

                      Dmitriy,
                      The SAMSON Team, https://s-c.io

                      1 Reply Last reply Reply Quote 0
                      • C
                        Carmine last edited by

                        @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.

                        DmitriyMarin 1 Reply Last reply Reply Quote 1
                        • DmitriyMarin
                          DmitriyMarin @Carmine last edited by

                          @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.

                          Dmitriy,
                          The SAMSON Team, https://s-c.io

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