On 2/27/15 7:16 PM, Nima Soltani wrote:
Excuse me that I forgot to attach the complete Error page:
nima@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....@gmail.com>
Date: Sat, Feb 28, 2015 at 3:34 AM
Subject: Umbrella sampling Tutorial Fatal Error
To: gmx-us...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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