[gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36
Quin K
profiles.ke at gmail.com
Wed Aug 28 16:29:40 CEST 2019
Thank you!
On Wed, Aug 28, 2019 at 7:56 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/28/19 10:21 AM, Quin K wrote:
> > *Thank you!*
> >
> > *When I use following in add ion step for tutorial (ion.mdp) it gives a
> > fatal error, however when I used cutoff instead of PME for couloumb type
> it
> > works with a note saying I should change it to PME. Any idea why?*
>
> This is addressed in the tutorial and in
>
> https://www.livecomsjournal.org/article/5068-from-proteins-to-perturbed-hamiltonians-a-suite-of-tutorials-for-the-gromacs-2018-molecular-simulation-package-article-v1-0
>
> You're just adding ions, so the physics are irrelevant. It doesn't
> matter if you're using a plain cutoff (never do this for a real
> simulation).
>
> -Justin
>
> > *ion.mdp*
> > define = -DREST_ON -DSTEP4_0
> > integrator = steep
> > emtol = 1000.0
> > nsteps = 5000
> > nstlist = 10
> > cutoff-scheme = Verlet
> > rlist = 1.2
> > vdwtype = Cut-off
> > vdw-modifier = Force-switch
> > rvdw_switch = 1.0
> > rvdw = 1.2
> > coulombtype = pme
> > rcoulomb = 1.2
> > constraints = h-bonds
> > constraint_algorithm = LINCS
> >
> > *I get following *
> > Inspiron5559:~/MD$ gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top
> -o
> > ions.tpr
> > :-) GROMACS - gmx grompp, 2018.1 (-:
> >
> > GROMACS is written by:
> > Emile Apol Rossen Apostolov Paul Bauer Herman J.C.
> > Berendsen
> > Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton
> Feenstra
> > Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca
> Hamuraru
> > Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri
> Kraus
> >
> > Carsten Kutzner Per Larsson Justin A. Lemkul Viveca
> Lindahl
> > Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu
> Murtola
> > Szilard Pall Sander Pronk Roland Schulz Alexey
> Shvetsov
> > Michael Shirts Alfons Sijbers Peter Tieleman Teemu
> Virolainen
> > 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) 2001-2017, 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 2018.1
> > Executable: /usr/bin/gmx
> > Data prefix: /usr
> > Working dir: /home/kelum/MD
> > Command line:
> > gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
> >
> > Setting the LD random seed to -1140183276
> > Generated 100032 of the 100128 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 1
> > Generated 65937 of the 100128 1-4 parameter combinations
> > Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> > turning H bonds into constraints...
> > Excluding 2 bonded neighbours molecule type 'SOL'
> > turning H bonds into constraints...
> >
> > NOTE 1 [file topol.top, line 43456]:
> > System has non-zero total charge: -2.000000
> > 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.
> >
> > WARNING 1 [file topol.top, line 43456]:
> > You are using Ewald electrostatics in a system with net charge. This
> can
> > lead to severe artifacts, such as ions moving into regions with low
> > dielectric, due to the uniform background charge. We suggest to
> > neutralize your system with counter ions, possibly in combination
> with a
> > physiological salt concentration.
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
> > Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with
> a
> > Net
> > Charge
> > J. Chem. Theory Comput. 10 (2014) pp. 381-393
> > -------- -------- --- Thank You --- -------- --------
> >
> > Removing all charge groups because cutoff-scheme=Verlet
> > Analysing residue names:
> > There are: 282 Protein residues
> > There are: 21749 Water residues
> > Analysing Protein...
> > Number of degrees of freedom in T-Coupling group rest is 141978.00
> > Calculating fourier grid dimensions for X Y Z
> > Using a fourier grid of 80x80x80, spacing 0.111 0.111 0.111
> > Estimate for the relative computational load of the PME mesh part: 0.12
> > This run will generate roughly 5 Mb of data
> >
> > There was 1 note
> >
> > There was 1 warning
> >
> > -------------------------------------------------------
> > Program: gmx grompp, version 2018.1
> > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2406)
> >
> > Fatal error:
> > Too many warnings (1).
> > If you are sure all warnings are harmless, use the -maxwarn option.
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > kelum at Inspiron5559:~/MD$
> >
> > On Wed, Aug 28, 2019 at 5:23 PM Mohammadreza Niknam Hamidabad <
> > jj700physics at gmail.com> wrote:
> >
> >> Hi,
> >> The parameters you should use for CHARMM36 are provided here (As you
> >> mentioned in your mail):
> >> <
> >>
> http://manual.gromacs.org/documentation/2018/user-guide/force-fields.html#targetText=CHARMM%20(Chemistry%20at%20HARvard%20Macromolecular,CHARMM27%2C%20CHARMM36)%20force%20fields
> >> If you encounter some errors please, copy-paste them in your email and
> the
> >> commands you used.
> >> Besides, if you use the charmm36 you can use CHARMM-GUI. In your case,
> you
> >> should probably use the solution builder:
> >> Solution Builder <http://www.charmm-gui.org/?doc=input/solution>
> >> When you provide all the inputs and parameters, you can download the
> final
> >> files (including all the *.mdp files)
> >> I hope you find it useful.
> >>
> >> Best regards,
> >> Reza
> >>
> >>
> >> On Wed, Aug 28, 2019 at 1:22 PM Quin K <profiles.ke at gmail.com> wrote:
> >>
> >>> Hi
> >>>
> >>> Does anyone have *.mdp* files for Lysozyme in water (With CHARMM36 FF)
> >>> tutorial given in following link.
> >>> http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html
> >>> I want to try this for a project I'm doing.
> >>> There are 4 .mdp files
> >>> ions.mdp <http://www.mdtutorials.com/gmx/lysozyme/Files/ions.mdp>
> >>> minim.mdp <http://www.mdtutorials.com/gmx/lysozyme/Files/minim.mdp>
> >>> nvt.mdp
> >>> npt.mdp <http://www.mdtutorials.com/gmx/lysozyme/Files/npt.mdp>
> >>>
> >>> I have tried to change the parameter files for CHARMM36 but did not
> >>> succeed.
> >>> CHARRM36
> >>> <
> >>>
> http://manual.gromacs.org/documentation/2018/user-guide/force-fields.html#targetText=CHARMM%20(Chemistry%20at%20HARvard%20Macromolecular,CHARMM27%2C%20CHARMM36)%20force%20fields
> >>> Thank you in advance!!
> >>>
> >>> Regards!
> >>> --
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> >>>
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> >>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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