[gmx-users] destruction of the structure of a molecule in water after energy minimization
Saeed Nasiri
s.t.nasiri at gmail.com
Fri Jun 2 10:26:17 CEST 2017
>
> Dear *Justin*
>
> I checked all of the parameters again and again and I try that to prepare
> them similar to the opls itp files.
> However, the problem does not solve. Also, when the energy minimization
> has been run there is warning about 1-4 interaction. I think
> that the problem is related to this warning.
>
> Thank you so much in advanced for your help.
>
>
> " ....
> Step= 44, Dmax= 3.2e-01 nm, Epot= 1.06264e+09 Fmax= 1.09629e+10, atom=
> 13
> WARNING: Listed nonbonded interaction between particles 11 and 14
> at distance 2.004 which is larger than the table limit 2.000 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
> ... "
>
>
> ########## topol.top ################
> #include "oplsaa.ff/forcefield.itp"
>
>
> #include "ff_BMI.itp"
> #include "BMI.itp"
> #include "Cl.itp"
>
> ; Include water topology
> #include "oplsaa.ff/tip3p.itp"
>
> [system]
> BMI Cl
>
> [molecules]
> BMI 1
> Cl 1
>
> ######### BMI.itp #################
> [ moleculetype ]
> ; Name nrexcl
> BMI 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> 1 CW 1 BMI CW 1 -0.13 12.011
> 2 CW 1 BMI CW 2 -0.13 12.011
> 3 CR 1 BMI CR 3 -0.11 12.011
> 4 HCW 1 BMI HCW 4 0.21 1.008
> 5 HCW 1 BMI HCW 5 0.21 1.008
> 6 HCR 1 BMI HCR 6 0.21 1.008
> 7 NA 1 BMI NA 7 0.15 14.007
> 8 NA 1 BMI NA 8 0.15 14.007
> 9 C1 1 BMI C1 9 -0.17 12.011
> 10 H1 1 BMI H1 10 0.13 1.008
> 11 H1 1 BMI H1 11 0.13 1.008
> 12 C2 1 BMI C2 12 0.01 12.011
> 13 HC 1 BMI HC 13 0.06 1.008
> 14 HC 1 BMI HC 14 0.06 1.008
> 15 CS 1 BMI CS 15 -0.12 12.011
> 16 HC 1 BMI HC 16 0.06 1.008
> 17 HC 1 BMI HC 17 0.06 1.008
> 18 CT 1 BMI CT 18 -0.18 12.011
> 19 HC 1 BMI HC 19 0.06 1.008
> 20 HC 1 BMI HC 20 0.06 1.008
> 21 HC 1 BMI HC 21 0.06 1.008
> 22 C1 1 BMI C1 22 -0.17 12.011
> 23 H1 1 BMI H1 23 0.13 1.008
> 24 H1 1 BMI H1 24 0.13 1.008
> 25 H1 1 BMI H1 25 0.13 1.008
>
>
> [ bonds ]
> ; ai aj funct
> 1 2 6
> 1 4 6
> 1 7 6
>
> 2 5 6
> 2 8 6
>
> 3 6 6
> 3 7 6
> 3 8 6
>
> 7 22 6
>
> 8 9 6
>
> 9 10 6
> 9 11 6
> 9 12 6
>
> 12 13 6
> 12 14 6
> 12 15 6
>
> 15 16 6
> 15 17 6
> 15 18 6
>
> 18 19 6
> 18 20 6
> 18 21 6
>
> 22 23 6
> 22 24 6
> 22 25 6
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
>
> 1 8 1
> 1 6 1
> 1 23 1
> 1 24 1
> 1 25 1
> 1 9 1
>
> 2 6 1
> 2 7 1
> 2 10 1
> 2 11 1
> 2 12 1
> 2 22 1
>
> 3 1 1
> 3 5 1
> 3 4 1
> 3 23 1
> 3 24 1
> 3 25 1
> 3 10 1
> 3 11 1
> 3 12 1
>
> 4 22 1
> 4 5 1
> 4 8 1
>
> 5 7 1
> 5 9 1
>
> 6 22 1
> 6 9 1
>
> 7 8 1
> 7 9 1
>
> 8 22 1
> 8 13 1
> 8 14 1
> 8 15 1
>
> 9 16 1
> 9 17 1
> 9 18 1
>
> 10 13 1
> 10 14 1
> 10 15 1
>
> 11 13 1
> 11 14 1
> 11 15 1
>
> 12 19 1
> 12 20 1
> 12 21 1
>
> 13 16 1
> 13 17 1
> 13 18 1
>
> 14 16 1
> 14 17 1
> 14 18 1
>
> 16 19 1
> 16 20 1
> 16 21 1
>
> 17 19 1
> 17 20 1
> 17 21 1
>
> [ angles ]
> ; ai aj ak funct
>
> 1 7 22 1
> 1 7 3 1
> 1 2 5 1
> 1 2 8 1
>
> 2 1 4 1
> 2 1 7 1
> 2 8 3 1
> 2 8 9 1
>
> 3 7 22 1
> 3 8 9 1
>
> 4 1 7 1
>
> 5 2 8 1
>
> 6 3 7 1
> 6 3 8 1
>
> 7 22 23 1
> 7 22 24 1
> 7 22 25 1
> 7 3 8 1
>
> 8 9 10 1
> 8 9 11 1
> 8 9 12 1
>
> 9 12 13 1
> 9 12 14 1
> 9 12 15 1
>
> 10 9 11 1
> 10 9 12 1
>
> 11 9 12 1
>
> 12 15 16 1
> 12 15 17 1
> 12 15 18 1
>
> 13 12 14 1
> 13 12 15 1
>
> 14 12 15 1
>
> 15 18 19 1
> 15 18 20 1
> 15 18 21 1
>
> 16 15 17 1
> 16 15 18 1
>
> 17 15 18 1
>
> 19 18 20 1
> 19 18 21 1
>
> 20 18 21 1
>
> 23 22 24 1
> 23 22 25 1
>
> 24 22 25 1
>
>
> [ dihedrals ]
>
> ; ai aj ak al funct
>
> 1 2 8 3 5
> 1 2 8 9 5
> 1 7 3 6 5
> 1 7 22 23 5
> 1 7 22 24 5
> 1 7 22 25 5
> 1 7 3 6 5
> 1 7 3 8 5
>
> 2 1 7 22 5
> 2 1 7 3 5
> 2 8 3 6 5
> 2 8 3 7 5
> 2 8 9 10 5
> 2 8 9 11 5
> 2 8 9 12 5
>
> 3 7 1 4 5
> 3 7 22 23 5
> 3 7 22 24 5
> 3 7 22 25 5
> 3 8 2 5 5
> 3 8 9 10 5
> 3 8 9 11 5
> 3 8 9 12 5
>
> 4 1 2 5 5
> 4 1 2 8 5
> 4 1 7 22 5
>
> 5 2 1 7 5
> 5 2 8 9 5
>
> 6 3 7 22 5
> 6 3 8 9 5
>
> 7 3 8 9 5
> 7 1 2 8 5
>
> 8 3 7 22 5
> 8 9 12 13 5
> 8 9 12 14 5
> 8 9 12 15 5
>
> 9 12 15 16 5
> 9 12 15 17 5
> 9 12 15 18 5
>
> 10 9 12 13 5
> 10 9 12 14 5
> 10 9 12 15 5
>
> 11 9 12 13 5
> 11 9 12 14 5
> 11 9 12 15 5
>
> 12 15 18 19 5
> 12 15 18 20 5
> 12 15 18 21 5
>
> 13 12 15 16 5
> 13 12 15 17 5
> 13 12 15 18 5
>
> 14 12 15 16 5
> 14 12 15 17 5
> 14 12 15 18 5
>
> 16 15 18 19 5
> 16 15 18 20 5
> 16 15 18 21 5
>
> 17 15 18 19 5
> 17 15 18 20 5
> 17 15 18 21 5
>
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3
>
> 3 1 7 22 5 improper_CR_CW_NA_C1
> 3 8 2 9 5 improper_CR_CW_NA_C1
>
> 7 8 3 5 5 improper_NA_NA_CR_HCR
>
> 7 1 2 4 5 improper_NA_CW_CW_HCW
> 8 2 1 5 5 improper_NA_CW_CW_HCW
>
>
> ######## ff_BMI.itp ###############
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> ;1 3 yes 0.5 0.5
>
> [ atomtypes ]
> ; name bond_type mass charge ptype sigma epsilon
>
> C1 6 12.0110 -0.170 A 3.500 0.27614
> C2 6 12.0110 0.010 A 3.500 0.27614
> CE 6 12.0110 -0.050 A 3.500 0.27614
> CS 6 12.0110 -0.120 A 3.500 0.27614
> CT 6 12.0110 -0.180 A 3.500 0.27614
> CR 6 12.0110 -0.110 A 3.550 0.29288
> CW 6 12.0110 -0.130 A 3.550 0.29288
> HA 1 1.0080 0.210 A 2.420 0.12552
> HCR 1 1.0080 0.210 A 2.420 0.12552
> HCW 1 1.0080 0.210 A 2.420 0.12552
> HC 1 1.0080 0.060 A 2.500 0.12552
> H1 1 1.0080 0.130 A 2.500 0.12552
> NA 7 14.0070 0.150 A 3.250 0.71128
> Cl 1 35.4530 -1.000 A 3.650 0.83000
>
>
> [ bondtypes ]
>
> ; i j func b0(re/nm) kb (kj/molnm^2)
>
>
> HC CT 6 0.1090 -284500
> HC CS 6 0.1090 -284500
> HC C2 6 0.1090 -284500
> HC C1 6 0.1090 -284500
> H1 C1 6 0.1090 -284500
>
> CT CS 6 0.1529 224200
> CS C2 6 0.1529 224200
> C2 C1 6 0.1529 224200
>
> CR HCR 6 0.1080 -284500
> CW HCW 6 0.1080 -284500
> CR NA 6 0.1315 399200
> CW NA 6 0.1378 357400
> CW CW 6 0.1341 435200
> NA C1 6 0.1466 141000
>
>
> [ angletypes ]
> ; i j k type th/deg ka/kjmol-1
>
>
> CT CS C2 1 112.700 488.300
> CS C2 C1 1 112.700 488.300
> C2 C1 NA 1 112.700 488.300
>
> CS CT HC 1 110.700 313.800
> CT CS HC 1 110.700 313.800
> C2 CS HC 1 110.700 313.800
> C2 C1 H1 1 110.700 313.800
> C1 C2 HC 1 110.700 313.800
> CS C2 HC 1 110.700 313.800
>
> HC CT HC 1 107.800 276.100
> HC CS HC 1 107.800 276.100
> HC C2 HC 1 107.800 276.100
> H1 C1 H1 1 107.800 276.100
>
>
> CW NA CR 1 108.000 585.800
> CW NA C1 1 125.600 585.800
> CR NA C1 1 126.400 585.800
> NA CR HCR 1 125.100 292.900
> NA CR NA 1 109.800 585.800
> NA CW CW 1 107.100 585.800
> NA CW HCW 1 122.000 292.900
> CW CW HCW 1 130.900 292.900
> NA C1 H1 1 110.700 313.800
> NA C1 C2 1 112.700 488.300
>
> [ dihedraltypes ]
> ; i j k l type v1 v2 v3 v4
>
> HC CT CS HC 5 0.00000 0.00000 1.33050
> 0.00000
> HC CS C2 HC 5 0.00000 0.00000 1.33050
> 0.00000
> HC C2 C1 H1 5 0.00000 0.00000 1.33050
> 0.00000
>
> CT CS C2 HC 5 0.00000 0.00000 1.53130
> 0.00000
> CS C2 C1 H1 5 0.00000 0.00000 1.53130
> 0.00000
> C1 C2 CS HC 5 0.00000 0.00000 1.53130
> 0.00000
> C2 CS CT HC 5 0.00000 0.00000 1.53130
> 0.00000
> CT CS C2 C1 5 7.28000 -0.65690 1.16730
> 0.00000
>
> CW NA CR NA 5 0.00000 19.46000 0.00000
> 0.00000
> CW NA CR HCR 5 0.00000 19.46000 0.00000
> 0.00000
> C1 NA CR NA 5 0.00000 19.46000 0.00000
> 0.00000
> C1 NA CR HCR 5 0.00000 19.46000 0.00000
> 0.00000
> CR NA CW CW 5 0.00000 12.55000 0.00000
> 0.00000
> CR NA CW HCW 5 0.00000 12.55000 0.00000
> 0.00000
> C1 NA CW CW 5 0.00000 12.55000 0.00000
> 0.00000
> C1 NA CW HCW 5 0.00000 12.55000 0.00000
> 0.00000
> NA CW CW NA 5 0.00000 44.98000 0.00000
> 0.00000
> NA CW CW HCW 5 0.00000 44.98000 0.00000
> 0.00000
> HCW CW CW HCW 5 0.00000 44.98000 0.00000
> 0.00000
> CW NA C1 H1 5 0.00000 0.00000 0.51900
> 0.00000
> CR NA C1 H1 5 0.00000 0.00000 0.00000
> 0.00000
> CW NA C1 C2 5 -7.15350 6.10640 0.79390
> 0.00000
> CR NA C1 C2 5 -5.26910 0.00000 0.00000
> 0.00000
> NA C1 C2 CS 5 -7.47970 3.16420 -1.20260
> 0.00000
> NA C1 C2 HC 5 0.00000 0.00000 0.36700
> 0.00000
>
> [ dihedraltypes ]
>
>
> #define improper_CR_CW_NA_C1 0.00000 8.37000 0.00000 0.00000
> #define improper_NA_NA_CR_HCR 0.00000 9.20000 0.00000 0.00000
> #define improper_NA_CW_CW_HCW 0.00000 9.20000 0.00000 0.00000
>
> ###########################################################
>
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