[gmx-users] Problems with Ionic Liquid Simulations

Wed Apr 4 00:25:03 CEST 2018

Hi All,

I am currently trying to run a simulation on the ionic liquid 1-butyl-3-methyl-imidazolium hexafluorophosphate ([Bmim][PF6]), but have run into a few errors I am unable to solve.

I've used the following steps in my simulation so far:

a) Generated the required .pdb files for both the [Bmim] cation and [PF6] anion.

b) Modified the following parameters in the OPLS-AA force field:

  *   atomtypes.atp
  *   aminoacids.rtp
  *   ffbonded.itp
  *   ffnonbonded.itp

 c)  Used Packmol to create a box containing a specific number of both the [Bmim] cations and [PF6] anions. This created the .pdb file [Bmim][PF6]

d) The generated .pdb file of the box from Packmol was then used with the pdb2gmx command to create the topol.top and .gro files.

e) Used the grompp command to assemble the structure, topology, and simulation parameters into a binary input file (.tpr) in order to be used for the energy minimisation. This was done via the following command:

gmx grompp -f minim.mdp -c bmimpf6_web_box.gro -p topol.top -o em.tpr

After inputting this command, the following errors were received:

WARNING 1 [file ffbonded.itp, line 2705]:
  Overriding Bond parameters.

  old: 0.1495 265266 0.1495 265266
  new: CS    CT      1    0.15290   224200.0

WARNING 2 [file ffbonded.itp, line 2706]:
  Overriding Bond parameters.

  old: 0.1343 399154 0.1343 399154
  new: CR    NA      1    0.13150   399200.0

WARNING 3 [file ffbonded.itp, line 2708]:
  Overriding Bond parameters.

  old: 0.1381 357314 0.1381 357314
  new: CW    NA      1    0.13780   357400.0

WARNING 4 [file ffbonded.itp, line 2712]:
  Overriding Bond parameters.

  old: 0.109 284512 0.109 284512
  new: CT    HC      1    0.10900   284500.0

WARNING 5 [file ffbonded.itp, line 2714]:
  Overriding Bond parameters.

  old: 0.1375 428442 0.1375 428442
  new: CW    CW      1    0.13410   435200.0

WARNING 6 [file ffbonded.itp, line 2716]:
  Overriding Bond parameters.

  old: 0.108 307106 0.108 307106
  new: CR    HA      1    0.10800   284500.0

WARNING 7 [file ffbonded.itp, line 2718]:
  Overriding Bond parameters.

  old: 0.108 307106 0.108 307106
  new: CW    HA      1    0.10800   284500.0

WARNING 8 [file ffbonded.itp, line 2722]:
  Overriding Angle parameters.

  old: 120 585.76 120 585.76
  new: NA     CR     NA      1   109.800    585.800

WARNING 9 [file ffbonded.itp, line 2727]:
  Overriding Angle parameters.

  old: 107.8 276.144 107.8 276.144
  new: HC     CT     HC      1   107.800    276.100

WARNING 10 [file ffbonded.itp, line 2730]:
  Overriding Angle parameters.

  old: 109.8 585.76 109.8 585.76
  new: CR     NA     CW      1   108.000    585.800

WARNING 11 [file ffbonded.itp, line 2733]:
  Overriding Angle parameters.

  old: 120 585.76 120 585.76
  new: CW     CW     NA      1   107.100    585.800

WARNING 12 [file ffbonded.itp, line 2740]:
  Overriding Angle parameters.

  old: 120 292.88 120 292.88
  new: HA     CR     NA      1   125.100    292.900

WARNING 13 [file ffbonded.itp, line 2741]:
  Overriding Angle parameters.

  old: 109.5 292.88 109.5 292.88
  new: CS     CT     HC      1   110.700    313.800

WARNING 14 [file ffbonded.itp, line 2743]:
  Overriding Angle parameters.

  old: 121.6 292.88 121.6 292.88
  new: HA     CW     NA      1   122.000    292.900

WARNING 15 [file ffbonded.itp, line 2755]:
  Overriding Ryckaert-Bell. parameters.

  old: 19.4556 0 -19.4556 0 0 0 19.4556 0 -19.4556 0 0 0
  new: HA     CR     NA     CW      3      0.00000  19.46000   0.00000   0.00000   0.00000   0.00000

WARNING 16 [file ffbonded.itp, line 2756]:
  Overriding Ryckaert-Bell. parameters.

  old: 13.3888 0 -13.3888 0 0 0 13.3888 0 -13.3888 0 0 0
  new: HA     CW     NA     CR      3      0.00000  12.55000   0.00000   0.00000   0.00000   0.00000

WARNING 17 [file ffbonded.itp, line 2765]:
  Overriding Ryckaert-Bell. parameters.

  old: 41.84 0 -41.84 0 0 0 41.84 0 -41.84 0 0 0
  new: NA     CR     NA     CW      3      0.00000  19.46000   0.00000   0.00000   0.00000   0.00000

WARNING 18 [file ffbonded.itp, line 2772]:
  Overriding Ryckaert-Bell. parameters.

  old: 13.3888 0 -13.3888 0 0 0 13.3888 0 -13.3888 0 0 0
  new: CW     CW     NA     CR      3      0.00000  12.55000   0.00000   0.00000   0.00000   0.00000

Generated 340725 of the 340725 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 340725 of the 340725 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Other_chain_A'
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   500      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 23997.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x36, 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 1 Mb of data

There was 1 note

There were 18 warnings

-------------------------------------------------------
Program gmx, VERSION 5.0
Source code file: /home/page/source/gromacs-5.0/src/gromacs/gmxpreprocess/grompp.c, line: 2087

Fatal error:
Too many warnings (18), gmx terminated.
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

Am I getting these errors because there are now two sets of values for these parameters in the ffbonded.itp file? And if so, should I just use the -maxwarn option to continue to the next step? I've looked around, and I have not been able to find an answer to this problem.

Thanks in advance everyone.

Regards,

JOSHUA Cummings
PhD Candidate
BSc (Chem)(Hons)
The Priority Research Centre for Frontier Energy Technologies and Utilisation
School of Chemical Engineering
Newcastle Institute for Energy and Resources (NIER)
T: +61 (0)2 4033 9244
M: +61 (0)4 2325 7078
E: Joshua.Cummings at uon.edu.au
The University of Newcastle (UON)
University Drive
Callaghan NSW 2308
Australia