[gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36

Wed Aug 28 16:26:15 CEST 2019

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
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>   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
>
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> Copyright (c) 2001-2017, The GROMACS development team at
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> check out http://www.gromacs.org for more information.
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> 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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