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

Quin K profiles.ke at gmail.com
Wed Aug 28 16:21:35 CEST 2019 

*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?*

*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!
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>

More information about the gromacs.org_gmx-users mailing list