[gmx-users] Problems with Ionic Liquid Simulations

Justin Lemkul jalemkul at vt.edu
Wed Apr 4 14:34:08 CEST 2018 


On 4/3/18 6:24 PM, Joshua Cummings wrote:
> 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.

Yes, you're providing parameter values that conflict with existing 
values in the force field. If you've got a source of custom parameters 
that have been previously validated, it may be a cleaner approach to 
make a totally different set of force field files, rather than trying to 
hack the existing OPLS-AA files, which could break other simulations 
down the road.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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