Hello Justin and thank you for your kind update and concern,
i.) What is the nature of the problems you are having?
I am struggling with obtaining the lipid area output via the 26 iteration Bash Script input.
I firstly input:
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr
gmx mdrun -deffnm system_inflated_em
gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro -pbc mol
mv tmp.gro system_inflated_em.gro
and then saved the Bash Script naming it run_inflategro.sh and then ran this script by inputting ./run_inflategro.sh
my results are halting at ITERATION 2, below is a paste starting with my Tutorial2 Folder in case needed to scan and then the output exhibiting the system_shrink1_em.tpr/gro errors. It is probably just something simple that needs to be changed that I am just not experienced yet to pick up on, any help would be great, thanks a bunch:)
Last login: Tue Sep 8 14:59:45 on ttys000
joelsubach@Joels-MacBook-Pro ~ % cd desktop
joelsubach@Joels-MacBook-Pro desktop %
joelsubach@Joels-MacBook-Pro desktop % cd tutorial2
joelsubach@Joels-MacBook-Pro tutorial2 % ls
#system_inflated_em.edr.1# #system_inflated_em.log.14# #tmp.gro.12#
#system_inflated_em.edr.10# #system_inflated_em.log.15# #tmp.gro.13#
#system_inflated_em.edr.11# #system_inflated_em.log.16# #tmp.gro.14#
#system_inflated_em.edr.12# #system_inflated_em.log.17# #tmp.gro.15#
#system_inflated_em.edr.13# #system_inflated_em.log.18# #tmp.gro.16#
#system_inflated_em.edr.14# #system_inflated_em.log.19# #tmp.gro.17#
#system_inflated_em.edr.15# #system_inflated_em.log.2# #tmp.gro.2#
#system_inflated_em.edr.16# #system_inflated_em.log.20# #tmp.gro.3#
#system_inflated_em.edr.17# #system_inflated_em.log.3# #tmp.gro.4#
#system_inflated_em.edr.18# #system_inflated_em.log.4# #tmp.gro.5#
#system_inflated_em.edr.19# #system_inflated_em.log.5# #tmp.gro.6#
#system_inflated_em.edr.2# #system_inflated_em.log.6# #tmp.gro.7#
#system_inflated_em.edr.20# #system_inflated_em.log.7# #tmp.gro.8#
#system_inflated_em.edr.3# #system_inflated_em.log.8# #tmp.gro.9#
#system_inflated_em.edr.4# #system_inflated_em.log.9# KALP-15_princ.pdb
#system_inflated_em.edr.5# #system_inflated_em.tpr.1# KALP-15_processed.gro
#system_inflated_em.edr.6# #system_inflated_em.tpr.2# KALP_newbox.gro
#system_inflated_em.edr.7# #system_inflated_em.tpr.3# area.dat
#system_inflated_em.edr.8# #system_inflated_em.tpr.4# area_shrink1.dat
#system_inflated_em.edr.9# #system_inflated_em.tpr.5# dppc.itp
#system_inflated_em.gro.1# #system_inflated_em.tpr.6# dppc.tpr
#system_inflated_em.gro.10# #system_inflated_em.tpr.7# dppc128.pdb
#system_inflated_em.gro.11# #system_inflated_em.trr.1# dppc128_whole.gro
#system_inflated_em.gro.12# #system_inflated_em.trr.10# gromos53a6_lipid.ff
#system_inflated_em.gro.13# #system_inflated_em.trr.11# inflategro.pl
#system_inflated_em.gro.14# #system_inflated_em.trr.12# lipid.itp
#system_inflated_em.gro.15# #system_inflated_em.trr.13# mdout.mdp
#system_inflated_em.gro.16# #system_inflated_em.trr.14# minim.mdp
#system_inflated_em.gro.17# #system_inflated_em.trr.15# minim_inflategro.mdp
#system_inflated_em.gro.18# #system_inflated_em.trr.16# posre.itp
#system_inflated_em.gro.19# #system_inflated_em.trr.17# run_inflategro.sh
#system_inflated_em.gro.2# #system_inflated_em.trr.18# strong_posre.itp
#system_inflated_em.gro.20# #system_inflated_em.trr.19# system.gro
#system_inflated_em.gro.3# #system_inflated_em.trr.2# system_inflated.gro
#system_inflated_em.gro.4# #system_inflated_em.trr.20# system_inflated_em.
#system_inflated_em.gro.5# #system_inflated_em.trr.3# system_inflated_em.edr
#system_inflated_em.gro.6# #system_inflated_em.trr.4# system_inflated_em.gro
#system_inflated_em.gro.7# #system_inflated_em.trr.5# system_inflated_em.log
#system_inflated_em.gro.8# #system_inflated_em.trr.6# system_inflated_em.tpr
#system_inflated_em.gro.9# #system_inflated_em.trr.7# system_inflated_em.trr
#system_inflated_em.log.1# #system_inflated_em.trr.8# system_shrink1.gro
#system_inflated_em.log.10# #system_inflated_em.trr.9# topol.top
#system_inflated_em.log.11# #tmp.gro.1# topol_dppc.top
#system_inflated_em.log.12# #tmp.gro.10#
#system_inflated_em.log.13# #tmp.gro.11#
joelsubach@Joels-MacBook-Pro tutorial2 % ./run_inflategro.sh
:-) GROMACS - gmx grompp, 2020.3-MODIFIED (-:
GROMACS is written by:
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 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 © 1991-2000, University of Groningen, The Netherlands.
Copyright © 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 2020.3-MODIFIED
Executable: /usr/local/bin/…/Cellar/gromacs/2020.3/bin/gmx
Data prefix: /usr/local/bin/…/Cellar/gromacs/2020.3
Working dir: /Users/joelsubach/Desktop/Tutorial2
Command line:
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr
Ignoring obsolete mdp entry ‘ns_type’
NOTE 1 [file minim_inflategro.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 -638078194
Generated 825 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 3 bonded neighbours molecule type ‘DPPC’
WARNING 1 [file topol.top, line 929]:
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 929]:
System has non-zero total charge: 4.000000
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.
Analysing residue names:
There are: 17 Protein residues
There are: 126 Other residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 19311.00
NOTE 3 [file minim_inflategro.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.
NOTE 4 [file minim_inflategro.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 1 Mb of data
There were 4 notes
There was 1 warning
Program: gmx grompp, version 2020.3-MODIFIED
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.
:-) GROMACS - gmx mdrun, 2020.3-MODIFIED (-:
GROMACS is written by:
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 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 © 1991-2000, University of Groningen, The Netherlands.
Copyright © 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 mdrun, version 2020.3-MODIFIED
Executable: /usr/local/bin/…/Cellar/gromacs/2020.3/bin/gmx
Data prefix: /usr/local/bin/…/Cellar/gromacs/2020.3
Working dir: /Users/joelsubach/Desktop/Tutorial2
Command line:
gmx mdrun -deffnm system_inflated_em
Compiled SIMD: AVX_256, but for this host/run AVX2_256 might be better (see
log).
Reading file system_inflated_em.tpr, VERSION 2020.3-MODIFIED (single precision)
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 8 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 1000 in 67 steps
Potential Energy = -9.5698570e+04
Maximum force = 8.4747546e+02 on atom 80
Norm of force = 6.5620194e+01
GROMACS reminds you: “Your Shopping Techniques are Amazing” (Gogol Bordello)
:-) GROMACS - gmx trjconv, 2020.3-MODIFIED (-:
GROMACS is written by:
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 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 © 1991-2000, University of Groningen, The Netherlands.
Copyright © 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 trjconv, version 2020.3-MODIFIED
Executable: /usr/local/bin/…/Cellar/gromacs/2020.3/bin/gmx
Data prefix: /usr/local/bin/…/Cellar/gromacs/2020.3
Working dir: /Users/joelsubach/Desktop/Tutorial2
Command line:
gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro -pbc mol
Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write gro: Coordinate file in Gromos-87 format
Reading file system_inflated_em.tpr, VERSION 2020.3-MODIFIED (single precision)
Reading file system_inflated_em.tpr, VERSION 2020.3-MODIFIED (single precision)
Select group for output
Group 0 ( System) has 6438 elements
Group 1 ( Protein) has 138 elements
Group 2 ( Protein-H) has 109 elements
Group 3 ( C-alpha) has 16 elements
Group 4 ( Backbone) has 48 elements
Group 5 ( MainChain) has 64 elements
Group 6 ( MainChain+Cb) has 78 elements
Group 7 ( MainChain+H) has 81 elements
Group 8 ( SideChain) has 57 elements
Group 9 ( SideChain-H) has 45 elements
Group 10 ( Prot-Masses) has 138 elements
Group 11 ( non-Protein) has 6300 elements
Group 12 ( Other) has 6300 elements
Group 13 ( DPPC) has 6300 elements
Select a group: Selected 0: ‘System’
Reading frames from gro file ‘frame t= 1.000’, 6438 atoms.
Reading frame 0 time 1.000
Precision of system_inflated_em.gro is 0.001 (nm)
Last frame 0 time 1.000
GROMACS reminds you: “Do You Have Sex Maniacs or Schizophrenics or Astrophysicists in Your Family?” (Gogol Bordello)
########################################
RUNNING SHRINKING ITERATION 1…
########################################
Reading…
Scaling lipids…
There are 126 lipids…
with 50 atoms per lipid…
Determining upper and lower leaflet…
63 lipids in the upper…
63 lipids in the lower leaflet
Centering protein…
Writing scaled bilayer & centered protein…
Calculating Area per lipid…
Protein X-min/max: 122 136
Protein Y-min/max: 122 135
X-range: 14 A Y-range: 13 A
Building 14 X 13 2D grid on protein coordinates…
Calculating area occupied by protein…
full TMD…
upper TMD…
lower TMD…
Area per protein: 2 nm^2
Area per lipid: 9.44753187580952 nm^2
Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 9.45150012977778 nm^2
Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 9.44753187580952 nm^2
Writing Area per lipid…
Done!
:-) GROMACS - gmx grompp, 2020.3-MODIFIED (-:
GROMACS is written by:
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 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 © 1991-2000, University of Groningen, The Netherlands.
Copyright © 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 2020.3-MODIFIED
Executable: /usr/local/bin/…/Cellar/gromacs/2020.3/bin/gmx
Data prefix: /usr/local/bin/…/Cellar/gromacs/2020.3
Working dir: /Users/joelsubach/Desktop/Tutorial2
Command line:
gmx grompp -f minim_inflategro.mdp -c system_shrink1.gro -r system_shrink1.gro -p topol.top -o system_shrink1_em.tpr
Ignoring obsolete mdp entry ‘ns_type’
NOTE 1 [file minim_inflategro.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 -108620144
Generated 825 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 3 bonded neighbours molecule type ‘DPPC’
WARNING 1 [file topol.top, line 929]:
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 929]:
System has non-zero total charge: 4.000000
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.
Analysing residue names:
There are: 17 Protein residues
There are: 126 Other residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 19311.00
NOTE 3 [file minim_inflategro.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.
NOTE 4 [file minim_inflategro.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
This run will generate roughly 1 Mb of data
There were 4 notes
There was 1 warning
Program: gmx grompp, version 2020.3-MODIFIED
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.
:-) GROMACS - gmx mdrun, 2020.3-MODIFIED (-:
GROMACS is written by:
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 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 © 1991-2000, University of Groningen, The Netherlands.
Copyright © 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 mdrun, version 2020.3-MODIFIED
Executable: /usr/local/bin/…/Cellar/gromacs/2020.3/bin/gmx
Data prefix: /usr/local/bin/…/Cellar/gromacs/2020.3
Working dir: /Users/joelsubach/Desktop/Tutorial2
Command line:
gmx mdrun -deffnm system_shrink1_em
Program: gmx mdrun, version 2020.3-MODIFIED
Source file: src/gromacs/options/options.cpp (line 179)
Function: void gmx::internal::OptionSectionImpl::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file ‘topol’ does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
:-) GROMACS - gmx trjconv, 2020.3-MODIFIED (-:
GROMACS is written by:
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 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 © 1991-2000, University of Groningen, The Netherlands.
Copyright © 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 trjconv, version 2020.3-MODIFIED
Executable: /usr/local/bin/…/Cellar/gromacs/2020.3/bin/gmx
Data prefix: /usr/local/bin/…/Cellar/gromacs/2020.3
Working dir: /Users/joelsubach/Desktop/Tutorial2
Command line:
gmx trjconv -s system_shrink1_em.tpr -f system_shrink1_em.gro -o tmp.gro -pbc mol
Program: gmx trjconv, version 2020.3-MODIFIED
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -s
File ‘system_shrink1_em.tpr’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -f
File ‘system_shrink1_em.gro’ does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
mv: rename tmp.gro to system_shrink1_em.gro: No such file or directory
########################################
RUNNING SHRINKING ITERATION 2…
########################################
system_shrink1_em.gro does not exist! Exiting.
joelsubach@Joels-MacBook-Pro tutorial2 %