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 (-:

GROMACS is written by:

Andrey Alekseenko Emile Apol Rossen Apostolov

Paul Bauer Herman J.C. Berendsen Par Bjelkmar

Christian Blau Viacheslav Bolnykh Kevin Boyd

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

Szilard Pall Sander Pronk Roland Schulz

Michael Shirts Alexey Shvetsov Alfons Sijbers

Peter Tieleman Jon Vincent Teemu Virolainen

Christian Wennberg Maarten Wolf Artem Zhmurov

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) 2001-2019, 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 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