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