[gmx-users] Problems with Ionic Liquid Simulations
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: CSCT 10.15290 224200.0 WARNING 2 [file ffbonded.itp, line 2706]: Overriding Bond parameters. old: 0.1343 399154 0.1343 399154 new: CRNA 10.13150 399200.0 WARNING 3 [file ffbonded.itp, line 2708]: Overriding Bond parameters. old: 0.1381 357314 0.1381 357314 new: CWNA 10.13780 357400.0 WARNING 4 [file ffbonded.itp, line 2712]: Overriding Bond parameters. old: 0.109 284512 0.109 284512 new: CTHC 10.10900 284500.0 WARNING 5 [file ffbonded.itp, line 2714]: Overriding Bond parameters. old: 0.1375 428442 0.1375 428442 new: CWCW 10.13410 435200.0 WARNING 6 [file ffbonded.itp, line 2716]: Overriding Bond parameters. old: 0.108 307106 0.108 307106 new: CRHA 10.10800 284500.0 WARNING 7 [file ffbonded.itp, line 2718]: Overriding Bond parameters. old: 0.108 307106 0.108 307106 new: CWHA 10.10800 284500.0 WARNING 8 [file ffbonded.itp, line 2722]: Overriding Angle parameters. old: 120 585.76 120 585.76 new: NA CR NA 1 109.800585.800 WARNING 9 [file ffbonded.itp, line 2727]: Overriding Angle parameters. old: 107.8 276.144 107.8 276.144 new: HC CT HC 1 107.800276.100 WARNING 10 [file ffbonded.itp, line 2730]: Overriding Angle parameters. old: 109.8 585.76 109.8 585.76 new: CR NA CW 1 108.000585.800 WARNING 11 [file ffbonded.itp, line 2733]: Overriding Angle parameters. old: 120 585.76 120 585.76 new: CW CW NA 1 107.100585.800 WARNING 12 [file ffbonded.itp, line 2740]: Overriding Angle parameters. old: 120 292.88 120 292.88 new: HA CR NA 1 125.100292.900 WARNING 13 [file ffbonded.itp, line 2741]: Overriding Angle parameters. old: 109.5 292.88 109.5 292.88 new: CS CT HC 1 110.700313.800 WARNING 14 [file ffbonded.itp, line 2743]: Overriding Angle parameters. old: 121.6 292.88 121.6 292.88 new: HA CW NA 1 122.000292.900 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 0.0 19.46000 0.0 0.0 0.0 0.0 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 0.0 12.55000 0.0 0.0 0.0 0.0 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 0.0 19.46000 0.0 0.0 0.0 0.0 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 0.0 12.55000 0.0 0.0 0.0 0.0 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 l
Re: [gmx-users] Problems with Ionic Liquid Simulations
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: CSCT 10.15290 224200.0 WARNING 2 [file ffbonded.itp, line 2706]: Overriding Bond parameters. old: 0.1343 399154 0.1343 399154 new: CRNA 10.13150 399200.0 WARNING 3 [file ffbonded.itp, line 2708]: Overriding Bond parameters. old: 0.1381 357314 0.1381 357314 new: CWNA 10.13780 357400.0 WARNING 4 [file ffbonded.itp, line 2712]: Overriding Bond parameters. old: 0.109 284512 0.109 284512 new: CTHC 10.10900 284500.0 WARNING 5 [file ffbonded.itp, line 2714]: Overriding Bond parameters. old: 0.1375 428442 0.1375 428442 new: CWCW 10.13410 435200.0 WARNING 6 [file ffbonded.itp, line 2716]: Overriding Bond parameters. old: 0.108 307106 0.108 307106 new: CRHA 10.10800 284500.0 WARNING 7 [file ffbonded.itp, line 2718]: Overriding Bond parameters. old: 0.108 307106 0.108 307106 new: CWHA 10.10800 284500.0 WARNING 8 [file ffbonded.itp, line 2722]: Overriding Angle parameters. old: 120 585.76 120 585.76 new: NA CR NA 1 109.800585.800 WARNING 9 [file ffbonded.itp, line 2727]: Overriding Angle parameters. old: 107.8 276.144 107.8 276.144 new: HC CT HC 1 107.800276.100 WARNING 10 [file ffbonded.itp, line 2730]: Overriding Angle parameters. old: 109.8 585.76 109.8 585.76 new: CR NA CW 1 108.000585.800 WARNING 11 [file ffbonded.itp, line 2733]: Overriding Angle parameters. old: 120 585.76 120 585.76 new: CW CW NA 1 107.100585.800 WARNING 12 [file ffbonded.itp, line 2740]: Overriding Angle parameters. old: 120 292.88 120 292.88 new: HA CR NA 1 125.100292.900 WARNING 13 [file ffbonded.itp, line 2741]: Overriding Angle parameters. old: 109.5 292.88 109.5 292.88 new: CS CT HC 1 110.700313.800 WARNING 14 [file ffbonded.itp, line 2743]: Overriding Angle parameters. old: 121.6 292.88 121.6 292.88 new: HA CW NA 1 122.000292.900 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 0.0 19.46000 0.0 0.0 0.0 0.0 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 0.0 12.55000 0.0 0.0 0.0 0.0 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 0.0 19.46000 0.0 0.0 0.0 0.0 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 0.0 12.55000 0.0 0.0 0.0 0.0 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
