I am following Justin Lemkul's GROMACS simulation given on this website here for GROMACS.
I believe I have followed the process to the T. I would like to mention that in the "Generate Topology" section of the tutorial, he says to include
#ifdef POSRES_B #include "posre_Protein_chain_B.itp" #endif
However, this was already present in my posre_Protein_chain_B.itp file. However this statement was also present in my posre_Protein_chain_A.itp, posre_Protein_chain_C.itp, posre_Protein_chain_D.itp, posre_Protein_chain_E.itp files. For example, posre_Protein_chain_A.itp had
#ifdef POSRES_A #include "posre_Protein_chain_A.itp" #endif
in it. I have commented them out, so it now looks like:
; #ifdef POSRES_A ; #include "posre_Protein_chain_A.itp" ; #endif
Furthermore, every time I was asked to choose for N-terminus, I hit option 2: None, and everytime I was asked to choose a C-terminus, I hit option 0: COO-. This resulted in the system having a net negative charge I believe.
I don't think I have deviated anywhere else in this simulation. However, I am getting the error message in the attachment when I run
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
After running this command I received the following error message:
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 2020.5 Executable: /home/satyend/.local/bin/gmx Data prefix: /home/satyend/.local Working dir: /home/satyend/software/gromacs_gpu/umbrella-sampling-protofibril Command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry 'ns_type' NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 2139084382 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Excluding 3 bonded neighbours molecule type 'Protein_chain_C' Excluding 3 bonded neighbours molecule type 'Protein_chain_D' Excluding 3 bonded neighbours molecule type 'Protein_chain_E' Excluding 2 bonded neighbours molecule type 'SOL' WARNING 1 [file topol.top, line 54]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Since there are researchers actively working on validating GROMOS with modern integrators we have not yet removed the GROMOS force fields, but you should be aware of these issues and check if molecules in your system are affected before proceeding. Further information is available at https://redmine.gromacs.org/issues/2884 , and a longer explanation of our decision to remove physically incorrect algorithms can be found at https://doi.org/10.26434/chemrxiv.11474583.v1 . NOTE 2 [file topol.top, line 54]: System has non-zero total charge: -10.000000 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. Number of degrees of freedom in T-Coupling group rest is 67749.00 NOTE 3 [file ions.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes There was 1 warning ------------------------------------------------------- Program: gmx grompp, version 2020.5 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353) 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 ------------------------------------------------------- Analysing residue names: There are: 135 Protein residues There are: 10727 Water residues Analysing Protein... This run will generate roughly 3 Mb of data
This is the link to the
ions.mdp file Dr. Lemkul has provided: http://www.mdtutorials.com/gmx/umbrella/Files/ions.mdp.
What is going wrong here? I feel like I am running around in circles with this tutorial...
I appreciate any advice you have to offer!