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

[Justin Lemkul]

On 2/27/15 7:16 PM, Nima Soltani 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
>
>

The simple answer is you have not translated the options properly.  Refer to:

http://manual.gromacs.org/online/mdp_opt.html#pull

I have been somewhat hesitant to update the tutorial for 5.0 because of all the 
changes, and the tutorial is linked directly to one of my papers.  I have been 
considering what to do for some time.  I don't intend to update the tutorial for 
a while at least, just because I don't have the time to make the changes and 
verify its accuracy, so please just ask questions via the list.

-Justin

>
> 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.
> =================================
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================