Dear Gromacs Users and Developers, I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic liquid MD simulation using amber 99 force field. I got my topology from topolbuild v 1.3. I successfully minimized both cation and anion separately using cg and steep. Then I include the anion in the cation system using genbox. I got error from grompp like this: ------------------------------------------------------------------------------ Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Segmentation fault (core dumped) [a...@neox MD1]$ --------------------------------------------------------------------------------- Still cant find my answer in the mailing list. Sorry for the large post, but here's my .mdp and .top
--------------------------------------------------------------------------------- title = Conjugated-Gradients Energy Minimization ; Preprocessing cpp = /lib/cpp include = -I../top ; Parameters integrator = cg emtol = 1.0 nsteps = 5000 nstenergy = 100 nstxtcout = 100 xtc_grps = System energygrps = System ; Neighboursearching nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 constraints = none pbc = xyz ----------------------------------------------------------------------------------------------------- ; Topology from .mol2 file ; topolbuild version 1.3 ; Command line: ; topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME ; ; The force field files to be included #include "amber99.ff/forcefield.itp" [ moleculetype ] ; name nrexcl BMIM 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 CT 1 BMIM C 1 -0.17243 12.01100 ; -0.1724300 2 HC 1 BMIM H 1 0.07139 1.00800 ; -0.1010400 3 HC 1 BMIM H 1 0.05434 1.00800 ; -0.0467000 4 HC 1 BMIM H 1 0.05138 1.00800 ; 0.0046800 5 CT 1 BMIM C 2 0.02353 12.01100 ; 0.0282100 6 HC 1 BMIM H 2 0.02417 1.00800 ; 0.0523800 7 HC 1 BMIM H 2 0.02427 1.00800 ; 0.0766500 8 CT 1 BMIM C 3 0.01014 12.01100 ; 0.0867900 9 HC 1 BMIM H 3 0.03312 1.00800 ; 0.1199100 10 HC 1 BMIM H 3 0.02952 1.00800 ; 0.1494300 11 NA 1 BMIM N 4 0.05435 14.00670 ; 0.2037800 12 CC 1 BMIM C 4 -0.17380 12.01100 ; 0.0299800 13 H4 1 BMIM H 4 0.23709 1.00800 ; 0.2670700 14 NA 1 BMIM N 6 0.07275 14.00670 ; 0.3398200 15 CT 1 BMIM C 5 -0.07367 12.01100 ; 0.2661500 16 H1 1 BMIM H 5 0.10657 1.00800 ; 0.3727200 17 H1 1 BMIM H 5 0.09108 1.00800 ; 0.4638000 18 CC 1 BMIM C 6 -0.08433 12.01100 ; 0.3794700 19 H4 1 BMIM H 6 0.20500 1.00800 ; 0.5844700 20 CR 1 BMIM C 7 -0.02624 12.01100 ; 0.5582300 21 H5 1 BMIM H 7 0.21862 1.00800 ; 0.7768500 22 CT 1 BMIM C 8 -0.18403 12.01100 ; 0.5928200 23 H1 1 BMIM H 8 0.13823 1.00800 ; 0.7310500 24 H1 1 BMIM H 8 0.13886 1.00800 ; 0.8699100 25 H1 1 BMIM H 8 0.13010 1.00800 ; 1.0000100 ; total molecule charge = 1.0000100 [ bonds ] ; ai aj funct b0 kb 1 5 1 0.15260 259408. ; C- C 1 2 1 0.10900 284512. ; C- H 1 3 1 0.10900 284512. ; C- H 1 4 1 0.10900 284512. ; C- H 5 8 1 0.15260 259408. ; C- C 5 6 1 0.10900 284511. ; C- H 5 7 1 0.10900 284512. ; C- H 8 15 1 0.15260 259408. ; C- C 8 9 1 0.10900 284512. ; C- H 8 10 1 0.10900 284512. ; C- H 11 12 1 0.13850 353129. ; N- C 11 15 1 0.13850 353129. ; N- C 11 20 1 0.13850 353129. ; N- C 12 18 1 0.14000 392459. ; C- C 12 13 1 0.10800 307106. ; C- H 14 18 1 0.13850 353129. ; N- C 14 20 1 0.13850 353129. ; N- C 14 22 1 0.13850 353129. ; N- C 15 16 1 0.10900 284512. ; C- H 15 17 1 0.10900 284512. ; C- H 18 19 1 0.10800 307106. ; C- H 20 21 1 0.10800 307106. ; C- H 22 23 1 0.10900 284512. ; C- H 22 24 1 0.10900 284512. ; C- H 22 25 1 0.10900 284512. ; C- H [ pairs ] 2 8 1 ; H- C 2 6 1 ; H- H 2 7 1 ; H- H 3 8 1 ; H- C 3 6 1 ; H- H 3 7 1 ; H- H 4 8 1 ; H- C 4 6 1 ; H- H 4 7 1 ; H- H 1 15 1 ; C- C 1 9 1 ; C- H 1 10 1 ; C- H 6 15 1 ; H- C 6 9 1 ; H- H 6 10 1 ; H- H 7 15 1 ; H- C 7 9 1 ; H- H 7 10 1 ; H- H 5 11 1 ; C- N 5 16 1 ; C- H 5 17 1 ; C- H 9 11 1 ; H- N 9 16 1 ; H- H 9 17 1 ; H- H 10 11 1 ; H- N 10 16 1 ; H- H 10 17 1 ; H- H 15 18 1 ; C- C 15 13 1 ; C- H 20 13 1 ; C- H 12 8 1 ; C- C 12 16 1 ; C- H 12 17 1 ; C- H 20 8 1 ; C- C 20 16 1 ; C- H 20 17 1 ; C- H 12 21 1 ; C- H 15 14 1 ; C- N 15 21 1 ; C- H 11 19 1 ; N- H 13 14 1 ; H- N 13 19 1 ; H- H 20 19 1 ; C- H 22 12 1 ; C- C 22 19 1 ; C- H 18 21 1 ; C- H 22 11 1 ; C- N 22 21 1 ; C- H 18 23 1 ; C- H 18 24 1 ; C- H 18 25 1 ; C- H 20 23 1 ; C- H 20 24 1 ; C- H 20 25 1 ; C- H [ angles ] ; ai aj ak funct th0 cth 2 1 5 1 109.500 418.4000 ; H- C- C 3 1 5 1 109.500 418.4000 ; H- C- C 4 1 5 1 109.500 418.4000 ; H- C- C 1 5 8 1 109.500 334.7200 ; C- C- C 1 5 6 1 109.500 418.4000 ; C- C- H 1 5 7 1 109.500 418.4000 ; C- C- H 3 1 2 1 109.500 292.8800 ; H- C- H 4 1 2 1 109.500 292.8800 ; H- C- H 4 1 3 1 109.500 292.8800 ; H- C- H 6 5 8 1 109.500 418.4000 ; H- C- C 7 5 8 1 109.500 418.4000 ; H- C- C 5 8 15 1 109.500 334.7200 ; C- C- C 5 8 9 1 109.500 418.4000 ; C- C- H 5 8 10 1 109.500 418.4000 ; C- C- H 7 5 6 1 109.500 292.8800 ; H- C- H 9 8 15 1 109.500 418.4000 ; H- C- C 10 8 15 1 109.500 418.4000 ; H- C- C 8 15 11 1 109.500 418.4000 ; C- C- N 8 15 16 1 109.500 418.4000 ; C- C- H 8 15 17 1 109.500 418.4000 ; C- C- H 10 8 9 1 109.500 292.8800 ; H- C- H 15 11 12 1 126.400 585.7600 ; C- N- C 20 11 12 1 120.000 585.7600 ; C- N- C 11 12 18 1 126.400 585.7600 ; N- C- C 11 12 13 1 120.000 418.4000 ; N- C- H 20 11 15 1 126.400 585.7600 ; C- N- C 11 15 16 1 109.500 418.4000 ; N- C- H 11 15 17 1 109.500 418.4000 ; N- C- H 11 20 14 1 120.000 585.7600 ; N- C- N 11 20 21 1 120.000 418.4000 ; N- C- H 13 12 18 1 120.000 418.4000 ; H- C- C 12 18 14 1 126.400 585.7600 ; C- C- N 12 18 19 1 120.000 418.4000 ; C- C- H 20 14 18 1 120.000 585.7600 ; C- N- C 22 14 18 1 126.400 585.7600 ; C- N- C 14 18 19 1 120.000 418.4000 ; N- C- H 22 14 20 1 120.000 585.7600 ; C- N- C 14 20 21 1 120.000 418.4000 ; N- C- H 14 22 23 1 109.500 418.4000 ; N- C- H 14 22 24 1 109.500 418.4000 ; N- C- H 14 22 25 1 109.500 418.4000 ; N- C- H 17 15 16 1 109.500 292.8800 ; H- C- H 24 22 23 1 109.500 292.8800 ; H- C- H 25 22 23 1 109.500 292.8800 ; H- C- H 25 22 24 1 109.500 292.8800 ; H- C- H [ dihedrals ] ; ai aj ak al funct phi0 cp mult 2 1 5 8 1 0.000 0.669 3 ; dih H- C- C- C 1 5 8 15 1 0.000 0.753 3 ; dih C- C- C- C 1 5 8 15 1 180.000 1.046 2 ; dih C- C- C- C 1 5 8 15 1 180.000 0.837 1 ; dih C- C- C- C 5 8 15 11 1 0.000 0.651 3 ; dih C- C- C- N 20 11 12 18 9 180.0 5.85760 2 ; dih C- N- C- C 12 11 15 8 1 0.000 0.000 2 ; dih C- N- C- C 12 11 20 14 9 180.0 5.85760 2 ; dih C- N- C- N 11 12 18 14 1 180.000 15.167 2 ; dih N- C- C- N 20 14 18 12 9 180.0 5.85760 2 ; dih C- N- C- C 18 14 20 11 9 180.0 5.85760 2 ; dih C- N- C- N 18 14 22 23 1 0.000 0.000 2 ; dih C- N- C- H 11 12 15 20 1 180.000 4.602 2 ; imp N- C- C- C 12 11 18 13 1 180.000 4.602 2 ; imp C- N- C- H 14 18 20 22 1 180.000 4.602 2 ; imp N- C- C- C 18 12 14 19 1 180.000 4.602 2 ; imp C- C- N- H 20 11 14 21 1 180.000 4.602 2 ; imp C- N- N- H ; Include Position restraint file ; WARNING: Position restraints and distance restraints ought not be done together #ifdef POSRES #include "posreBMIM_Test3.itp" #endif ; Include TFO topology #include TFO_amber99.itp ; Include water topology #include "tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; title from mol2 input BMIMTFO [ molecules ] ; molecule name nr. BMIM 1 TFO 1 -------------------------------------------------------------------------------------------- Any thought, advice and support is greatly appreciated. Thank you. -Alif-
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