Input command : gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index_ligand_au.ndx -t npt.cpt -o pull.tpr -maxwarn 3
:-) GROMACS - gmx grompp, 2021.4-Ubuntu-2021.4-2 (-:
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Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
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Michael Shirts Alexey Shvetsov Alfons Sijbers
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Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
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check out http://www.gromacs.org for more information.
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GROMACS: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/parul/umb_samp_iiserprac/final_attempt/take_3_au_ligand
Command line:
gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index_ligand_au.ndx -t npt.cpt -o pull.tpr -maxwarn 3
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'optimize_fft'
Ignoring obsolete mdp entry 'ns_type'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
NOTE 1 [file md_pull.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file md_pull.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Setting the LD random seed to -1091326221
Generated 222 of the 1653 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'AU'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Z9FE'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'AU'
Excluding 3 bonded neighbours molecule type 'Z9FE'
Excluding 1 bonded neighbours molecule type 'CL'
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
WARNING 1 [file topol.top, line 31]:
The following macros were defined in the 'define' mdp field with the -D
prefix, but were not used in the topology:
POSRES_Z9FE
If you haven't made a spelling error, either use the macro you defined,
or don't define the macro
WARNING 2 [file topol.top, line 31]:
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 .
Pull group 1 'Chain_A' has 4221 atoms
Pull group 2 'Chain_B' has 4221 atoms
Number of degrees of freedom in T-Coupling group Water is 1137693.00
Number of degrees of freedom in T-Coupling group non-Water is 19505.95
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.495 nm, buffer size 0.095 nm
Set rlist, assuming 4x4 atom pair-list, to 1.420 nm, buffer size 0.020 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame -1 time 100.000
Using frame at t = 100 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 168x168x144, spacing 0.117 0.117 0.109
ERROR 1 [file md_pull.mdp]:
When the maximum distance from a pull group reference atom to other atoms
in the group is larger than 0.5 times half the box size a centrally
placed atom should be chosen as pbcatom. Pull group 1 is larger than that
and does not have a specific atom selected as reference atom.
ERROR 2 [file md_pull.mdp]:
When the maximum distance from a pull group reference atom to other atoms
in the group is larger than 0.5 times half the box size a centrally
placed atom should be chosen as pbcatom. Pull group 2 is larger than that
and does not have a specific atom selected as reference atom.
Pull group natoms pbc atom distance at start reference at t=0
1 4221 2111
2 4221 6332 0.488 nm 0.488 nm
Estimate for the relative computational load of the PME mesh part: 0.10
NOTE 3 [file md_pull.mdp]:
This run will generate roughly 5408 Mb of data
There were 3 notes
There were 2 warnings
-------------------------------------------------------
Program: gmx grompp, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2389)
Fatal error:
There were 2 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Copy-pasting from previous answer (https://www.researchgate.net/post/Getting_error_in_Steered_Molecular_Dynamics_Simulation_in_GROMACS_2020)
This means that group 1 is very large and some atoms in that group are distant from each other more than 0.5 times the box size. This is a problem for GROMACS when it tries to calculate distances, since PBC are on and the true distance is not well defined anymore.
Try to visualize group 1 with some tool like VMD and try to find an atom that is ca. at the centre of your group 1. Take that atom number from the .gro/.pdb/your structure file and then add the option
pull-group1-pbcatom = #number_of_your_central_atom
to your mdp file (https://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#com-pulling).
When you do not specify this option, gromacs just searches for the central atom in the group from the list, i.e., if you have a group of 10 atoms gromacs uses the fifth, which does not correspond necessarily with the geometrical centre of your group. This usually is not a problem, but when groups are larger than half the box then the choice could be not ideal to calculate distances with PBC, and so you have to specify a better atom for gromacs to use.
Hope this helps,
Nicola
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