ERROR 1 [file npt_umbrella.mdp]: INQUIRY?

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1

GROMACS version: 2020.3
GROMACS modification: Yes/No
Here post your question

Step Six: Umbrella Sampling Simulations;
After having identified the initial configurations of the sampling windows, I am now preparing umbrella sampling simulations and received an error upon the generation of my 7th tpr output (see command below):

gmx grompp -f npt_umbrella.mdp -c conf204.gro -p topol.top -r conf204.gro -n index.ndx -o npt7.tpr

ERROR 1 [file npt_umbrella.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.

Pull group natoms pbc atom distance at start reference at t=0
1 226 113
2 226 339 1.887 nm 1.887 nm

prior to this I used the below command to identify the initial configurations of the sampling windows:

Perl get_distances.sh

I am not sure if the above command of execution is incorrect causing the above error?

If the Perl Command is correct suggestions please?

Thanks:)

2

This isn’t a valid command. The shell script calls a Perl script to parse distance information.

You shouldn’t get any errors when running the tutorial. Make sure you’ve set up the box properly.

3

Hello Justin and thank you for your kind update.:)

Yes I will then backtrack back to the generation of new summary_distances.dat output, please tell me what is the command to iteratively call gmx distance on all of the 501! frames, that were generated via the gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep, using the bash script get_distances.sh?

I am still quite new at Gromacs and did not see this specific command in either tutorial, I completed successfully Tutorials 1 and 2 and within 2 the perl command was specific, for example:

perl water_deletor.pl -in system_solv.gro -out system_solv_fix.gro -ref O33 -middle C50 -nwater 3

Thanks:)
Joel

4

Everything is in the bash script itself. The script just saves you from having to run everything manually.

5

Hello thank you and understandable but from my understanding from the tutorials I would execute this bash script subsequent to the command:

gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep

accordingly what would I input to execute this bash script if my above first command is correct?
(Or maybe this bash is within my above command, I am not sure.)

Any help would be appreciated:)

Best,
Joel

6

I’m sorry but I don’t understand what you’re asking. What you’ve posted is literally the first line of the script, which produces individual coordinate files. The script then loops over those and calculates the relevant distances.

7

Hello and ah ok understood and yes then I believe as i stated the bash script is executed via:

gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep

Thanks:)
Joel

8

Hello I repeated the commands:

saving the bash as: get_distances.sh

then input: gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep

outputting a summary_distances.dat which seems to have output the correct numbers i.e. at 0 time 0.506 nm, at 164 time 0.706 nm…at 500 time 5.491 distance.

However when again running subsequent:

gmx grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -r conf0.gro -n index.ndx -o npt0.tpr

my 7th npt.tpr run:
gmx grompp -f npt_umbrella.mdp -c conf205.gro -p topol.top -r conf205.gro -n index.ndx -o npt7.tpr -maxwarn 2
produces this same error:

ERROR 1 [file npt_umbrella.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.

I am still unsure if me just inputting the above gmx trjconv command executes the bash script, maybe this is the problem. Any suggestions would be appreciated, I inputted my box size correctly and the VMD visual confirmed this.

Best,
Joel

9

What are the box vectors in conf205.gro?

10

Hello and thank you for your inquiry,

conf205.gro box vectors: 6.58035 4.37553 12.03722

Also below is a paste of my complete output incase the output notes and warnings are precipitating this Fatal Error:

Joels-MacBook-Pro:tutorial3 joelsubach$ gmx grompp -f npt_umbrella.mdp -c conf205.gro -p topol.top -r conf205.gro -n index.ndx -o npt7.tpr -maxwarn 2
:-) 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 (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 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/Tutorial3
Command line:
gmx grompp -f npt_umbrella.mdp -c conf205.gro -p topol.top -r conf205.gro -n index.ndx -o npt7.tpr -maxwarn 2

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘optimize_fft’
Ignoring obsolete mdp entry ‘ns_type’

NOTE 1 [file npt_umbrella.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy

NOTE 2 [file npt_umbrella.mdp]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.

Setting the LD random seed to 1981139207
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
turning all bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_B’
turning all bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_C’
turning all bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_D’
turning all bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_E’
turning all bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘SOL’
turning all bonds into constraints…
Excluding 1 bonded neighbours molecule type ‘NA’
turning all bonds into constraints…
Excluding 1 bonded neighbours molecule type ‘CL’
turning all bonds into constraints…

WARNING 1 [file topol.top, line 56]:
The following macros were defined in the ‘define’ mdp field with the -D
prefix, but were not used in the topology:
POSRES_B
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 56]:
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
On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage .

Setting gen_seed to 1264030319
Velocities were taken from a Maxwell distribution at 310 K
Pull group 1 ‘Chain_A’ has 226 atoms
Pull group 2 ‘Chain_B’ has 226 atoms
Number of degrees of freedom in T-Coupling group Protein is 2254.90
Number of degrees of freedom in T-Coupling group non-Protein is 64203.10
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 1.419 nm, buffer size 0.019 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 56x40x104, spacing 0.118 0.109 0.116

ERROR 1 [file npt_umbrella.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.

Pull group natoms pbc atom distance at start reference at t=0
1 226 113
2 226 339 1.906 nm 1.906 nm
Estimate for the relative computational load of the PME mesh part: 0.11
This run will generate roughly 13 Mb of data

There were 2 notes

There were 2 warnings

Program: gmx grompp, version 2020.3-MODIFIED
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

Joels-MacBook-Pro:tutorial3 joelsubach$

11

Couple of things here:

  1. Don’t use -maxwarn 2. You are overriding a mistake you’ve made (likely a typo) that will yield incorrect behavior:
  1. The other issue is it appears that grompp has somehow changed the way it interprets the pull reference distance, according to the second warning. The tutorial was written and tested with version 2018, not version 2020. You also appear to be using some hacked version of 2020.3, so beware. I don’t know what modifications you’ve made but you should be doing tutorials with a clean version of the software that meets the requirements of the tutorial.
12

Hello Justin and thank you for your kind update,

Yes I saved and used the pulling mdp file as indicated (I copied and pasted):

title = Umbrella pulling simulation
define = -DPOSRES_B

and added the proper Position restraint file to topol_Protein_chain_B.itp as instructed i.e. Modify topol_Protein_chain_B.itp to include the following lines (at the end of the file copying and pasting):

; Include Position restraint file
#ifdef POSRES
#include “posre_Protein_chain_B.itp”
#endif

accordingly is the below WARNING inferring me to modify somehow my above pulling mdp and or topol_Protein_chain_B.itp?

WARNING 1 [file topol.top, line 56]:
The following macros were defined in the ‘define’ mdp field with the -D
prefix, but were not used in the topology:
POSRES_B
If you haven’t made a spelling error, either use the macro you defined,
or don’t define the macro

and or I agree maybe it is the second warning. I had paid assistance in installing 2020.3 via Homebrew which does not indicate that its installation script was hacked. Any assistance in working through this hiccup will be appreciated, much thanks:)

13

That’s supposed to be #ifdef POSRES_B - grompp is telling you that something in the .mdp file is unmatched in the topology. If you plowed through the same warning when setting up the windows, correct the mistake and do the pulling/window generation over again. You probably have a bad set of configurations that’s triggering the grompp warning.

I have no idea what Homebrew does or what package it has installed. But whenever the GROMACS code says “MODIFIED” in the version, that means it is not the normal code, so someone may have toyed with it. Install from source yourself rather than through a package manager; you will get better performance anyway than when using generic installs.

14

Hello and thank you for your kind update re-pulling now.:)

Justin how does the command:
gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep
intelligently execute the saved get_distances.sh Bash Script, does it do this via the code echo 0 within the first line of the bash?

Best,
Joel

15

Bash is an interpreter of commands. GROMACS doesn’t run bash, it’s the other way around. gmx trjconv in this instance generates individual coordinate files, which requires a selection. To automate that process, the shell uses echo to pass the selection value to gmx trjconv.

16

Hi and thanks, and in this case I believe the required selection value to be a pull file.

17

I’m afraid I don’t understand. Files aren’t passed to any selection mechanism in GROMACS.

18

Hi when you mentioned ´the shell uses echo to pass the selection value´ what would be an example of a selection value in this case to help me better understand, thanks:)

19

Exactly what’s in the script. echo 0 passes a value of 0 to gmx trjconv, which selects “System” from the list of choices.

20

Hi thanks a bunch:)