[gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error

Sat Feb 28 01:22:09 CET 2015

Hi,

Did you check the parameters in .mdp file for pulling simulation?!
I think you have to define this pulling group in .mdp file that you use in
grompp.

On Fri, Feb 27, 2015 at 7:16 PM, Nima Soltani <nima.slt at gmail.com> wrote:

> Excuse me that I forgot to attach the complete Error page:
> nima at nima-ThinkPad:~/Desktop/3$ gmx grompp -f md_pull.mdp -c npt.gro -p
> topol.top -n index.ndx -t npt.cpy -o pull.tpr
> GROMACS:    gmx grompp, VERSION 5.0.2
>
> GROMACS is written by:
> Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par
> Bjelkmar
> Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch
> Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner
> Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff
> Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk
> Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers
> Peter Tieleman     Christian Wennberg Maarten Wolf
> 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) 2001-2014, 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 5.0.2
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>   gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpy
> -o pull.tpr
>
>
> NOTE 1 [file md_pull.mdp, line 62]:
>   md_pull.mdp did not specify a value for the .mdp option "cutoff-scheme".
>   Probably it was first intended for use with GROMACS before 4.6. In 4.6,
>   the Verlet scheme was introduced, but the group scheme was still the
>   default. The default is now the Verlet scheme, so you will observe
>   different behaviour.
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'optimize_fft'
> Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
> ERROR: pull-coord1-groups should have 2 components
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
>
> WARNING 1 [file md_pull.mdp, line 62]:
>   Unknown left-hand 'pull_group0' in parameter file
>
>
>
> WARNING 2 [file md_pull.mdp, line 62]:
>   Unknown left-hand 'pull_group1' in parameter file
>
>
>
> WARNING 3 [file md_pull.mdp, line 62]:
>   Unknown left-hand 'pull_rate1' in parameter file
>
>
>
> WARNING 4 [file md_pull.mdp, line 62]:
>   Unknown left-hand 'pull_k1' in parameter file
>
>
>
> NOTE 2 [file md_pull.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.
>
>
> NOTE 3 [file md_pull.mdp]:
>   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>   nstcomm to nstcalcenergy
>
>
> NOTE 4 [file md_pull.mdp]:
>   leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to
> 1
>
> Setting the LD random seed to 1032180820
> 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...
> Removing all charge groups because cutoff-scheme=Verlet
> The center of mass of the position restraint coord's is  3.265  2.171
> 2.977
> The center of mass of the position restraint coord's is  3.265  2.171
> 2.977
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.2
> Source code file:
>
> /home/nima/Documents/Gromacs-Program/gromacs-5.0.2/src/gromacs/gmxpreprocess/readpull.c,
> line: 257
>
> Fatal error:
> Group pull_group1 required by grompp was undefined.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> Best Regards,
> Nima Soltani
> ----------------------------------------------------------
> Graduate Student of Physical Chemistry
> Department of Chemistry,
> Sharif University of Technology.
> =================================
>
> ---------- Forwarded message ----------
> From: Nima Soltani <nima.slt at gmail.com>
> Date: Sat, Feb 28, 2015 at 3:34 AM
> Subject: Umbrella sampling Tutorial Fatal Error
> To: gmx-users at gromacs.org
>
>
> Hi Dear Gromacs Users
> I am following umbrella sampling tutorial provided by Dr Justin Lemkul
> (This tutorial is not updated for Gromacs 5 However I am using Gromacs
> 5.0.2 and i am trying my best to use files and commands compatible with
> version 5)
>
> I have done all the parts up to pulling section very well
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
> but at the stage that I want to generate pull.tpr file it gives me a fatal
> Error:
> "Fatal error:
> Group pull_group1 required by grompp was undefined."
> I Checked spelling of "Chain_A" that i named, utilizing "mgx make_ndx"
> command at previous step
> Any advice or guidance would be greatly appreciated
> Best Regards,
> Nima Soltani
> ----------------------------------------------------------
> Graduate Student of Physical Chemistry
> Department of Chemistry,
> Sharif University of Technology.
> =================================
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