As noted in previous email and the warning message states, since you are simply trying to add the counter ions and not run a simulation get grompp to ignore the message and continue on i.e. add -maxwarn 1 to the command.
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 25 Jun 2019 at 00:19, kalpana <kalpanadyna...@gmail.com> wrote: > > Dear all, > I have worked with the same commands and setting in previous version of > ubuntu and gromacs. Now with new system and up-gradation, I am facing > problem. First kindly see the gmx information and then see the fatal error, > I am getting at grompp. Kindly find the attached ions.mdp as well and see > the other .mdp files too and guide me. > Thanks & Regards > Kalpana > > > 1. > gmx --version > > GROMACS version: 2019.3 > Precision: single > Memory model: 64 bit > MPI library: thread_mpi > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) > GPU support: CUDA > SIMD instructions: AVX_512 > FFT library: fftw-3.3.8-sse2-avx > RDTSCP usage: enabled > TNG support: enabled > Hwloc support: hwloc-1.11.6 > Tracing support: disabled > C compiler: /usr/bin/gcc GNU 8.3.0 > C compiler flags: -mavx512f -mfma -g -fno-inline > C++ compiler: /usr/bin/c++ GNU 8.3.0 > C++ compiler flags: -mavx512f -mfma -std=c++11 -g -fno-inline > CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler > driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on > Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1, V10.1.168 > CUDA compiler > flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;; > ;-mavx512f;-mfma;-std=c++11;-g;-fno-inline; > CUDA driver: 10.10 > CUDA runtime: N/A > > > 2. > gmx pdb2gmx -f 1model1A1.pdb -o model1_processed.gro -water tip3p > no warning and notes in pdb2gmx run > > 3. > gmx editconf -f model1_processed.gro -o model1_newbox.gro -c -d 1.0 -bt > dodecahedron > no warning and notes in editconf > > 4. > gmx solvate -cp model1_newbox.gro -cs spc216.gro -o model1_solv.gro -p > topol.top > > WARNING: Masses and atomic (Van der Waals) radii will be guessed > based on residue and atom names, since they could not be > definitively assigned from the information in your input > files. These guessed numbers might deviate from the mass > and radius of the atom type. Please check the output > files if necessary. > > NOTE: From version 5.0 gmx solvate uses the Van der Waals radii > from the source below. This means the results may be different > compared to previous GROMACS versions. > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > A. Bondi > van der Waals Volumes and Radii > J. Phys. Chem. 68 (1964) pp. 441-451 > -------- -------- --- Thank You --- -------- -------- > > 5. > gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr > > NOTE 1 [file topol.top, line 60959]: > System has non-zero total charge: -13.000000 > Total charge should normally be an integer. See > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > for discussion on how close it should be to an integer. > > WARNING 1 [file topol.top, line 60959]: > You are using Ewald electrostatics in a system with net charge. This can > lead to severe artifacts, such as ions moving into regions with low > dielectric, due to the uniform background charge. We suggest to > neutralize your system with counter ions, possibly in combination with a > physiological salt concentration. > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof > Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a > Net > Charge > J. Chem. Theory Comput. 10 (2014) pp. 381-393 > -------- -------- --- Thank You --- -------- -------- > > Removing all charge groups because cutoff-scheme=Verlet > Analysing residue names: > There are: 424 Protein residues > There are: 16060 Water residues > Analysing Protein... > Number of degrees of freedom in T-Coupling group rest is 115683.00 > Calculating fourier grid dimensions for X Y Z > Using a fourier grid of 80x80x80, spacing 0.116 0.116 0.116 > Estimate for the relative computational load of the PME mesh part: 0.34 > This run will generate roughly 4 Mb of data > > There was 1 note > > There was 1 warning > > ------------------------------------------------------- > Program: gmx grompp, version 2019.3 > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2315) > > Fatal error: > Too many warnings (1). > 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 > ------------------------------------------------------- > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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