Hello Justin, As for exclusions, in the manual I see 1-4 interactions refer to carbon atoms on the backbone. I do not know if it makes sense if I enter a number more than 5 (hexane has only 6 carbons), However, I did so and I changed nrexcl from default value of 3 to 19 ( to exlude all interactions between all C and H atoms!) but I got the following message after grompp em step:
checking input for internal consistency... Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 19 bonded neighbours molecule type 'Hexane' ------------------------------------------------------- Program grompp, VERSION 4.0.7 Source code file: smalloc.c, line: 147 Fatal error: Not enough memory. Failed to calloc 78089438 elements of size 8 for s (called from file topexcl.c, line 161) ------------------------------------------------------- I also tried another approach (although I am almost sure this is not the proper way of excluding ALL interactions as in this way I think I am excluding atom 1 and all other atoms only!) and added exclusions directive as you see below in top file ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Name nrexcl Hexane 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot -0.18 2 opls_140 1 HEX H11 1 0.06 1.008 ; qtot -0.12 3 opls_140 1 HEX H12 1 0.06 1.008 ; qtot -0.06 4 opls_140 1 HEX H13 1 0.06 1.008 ; qtot 0 5 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot -0.12 6 opls_140 1 HEX H21 2 0.06 1.008 ; qtot -0.06 7 opls_140 1 HEX H22 2 0.06 1.008 ; qtot 0 8 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot -0.12 9 opls_140 1 HEX H31 3 0.06 1.008 ; qtot -0.06 10 opls_140 1 HEX H32 3 0.06 1.008 ; qtot 0 11 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot -0.12 12 opls_140 1 HEX H41 4 0.06 1.008 ; qtot -0.06 13 opls_140 1 HEX H42 4 0.06 1.008 ; qtot 0 14 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot -0.12 15 opls_140 1 HEX H51 5 0.06 1.008 ; qtot -0.06 16 opls_140 1 HEX H52 5 0.06 1.008 ; qtot 0 17 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot -0.18 18 opls_140 1 HEX H61 6 0.06 1.008 ; qtot -0.12 19 opls_140 1 HEX H62 6 0.06 1.008 ; qtot -0.06 20 opls_140 1 HEX H63 6 0.06 1.008 ; qtot 0 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 5 8 1 8 9 1 8 10 1 8 11 1 11 12 1 11 13 1 11 14 1 14 15 1 14 16 1 14 17 1 17 18 1 17 19 1 17 20 1 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 9 1 1 10 1 1 11 1 2 6 1 2 7 1 2 8 1 3 6 1 3 7 1 3 8 1 4 6 1 4 7 1 4 8 1 5 12 1 5 13 1 5 14 1 6 9 1 6 10 1 6 11 1 7 9 1 7 10 1 7 11 1 8 15 1 8 16 1 8 17 1 9 12 1 9 13 1 9 14 1 10 12 1 10 13 1 10 14 1 11 18 1 11 19 1 11 20 1 12 15 1 12 16 1 12 17 1 13 15 1 13 16 1 13 17 1 15 18 1 15 19 1 15 20 1 16 18 1 16 19 1 16 20 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 1 2 1 4 1 2 1 5 1 3 1 4 1 3 1 5 1 4 1 5 1 1 5 6 1 1 5 7 1 1 5 8 1 6 5 7 1 6 5 8 1 7 5 8 1 5 8 9 1 5 8 10 1 5 8 11 1 9 8 10 1 9 8 11 1 10 8 11 1 8 11 12 1 8 11 13 1 8 11 14 1 12 11 13 1 12 11 14 1 13 11 14 1 11 14 15 1 11 14 16 1 11 14 17 1 15 14 16 1 15 14 17 1 16 14 17 1 14 17 18 1 14 17 19 1 14 17 20 1 18 17 19 1 18 17 20 1 19 17 20 1 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 5 6 3 2 1 5 7 3 2 1 5 8 3 3 1 5 6 3 3 1 5 7 3 3 1 5 8 3 4 1 5 6 3 4 1 5 7 3 4 1 5 8 3 1 5 8 9 3 1 5 8 10 3 1 5 8 11 3 6 5 8 9 3 6 5 8 10 3 6 5 8 11 3 7 5 8 9 3 7 5 8 10 3 7 5 8 11 3 5 8 11 12 3 5 8 11 13 3 5 8 11 14 3 9 8 11 12 3 9 8 11 13 3 9 8 11 14 3 10 8 11 12 3 10 8 11 13 3 10 8 11 14 3 8 11 14 15 3 8 11 14 16 3 8 11 14 17 3 12 11 14 15 3 12 11 14 16 3 12 11 14 17 3 13 11 14 15 3 13 11 14 16 3 13 11 14 17 3 11 14 17 18 3 11 14 17 19 3 11 14 17 20 3 15 14 17 18 3 15 14 17 19 3 15 14 17 20 3 16 14 17 18 3 16 14 17 19 3 16 14 17 20 3 ; Include Position restraint file ;#ifdef POSRES ;#include "posre.itp" ;#endif ; Include water topology ;#include "spc.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" *[ exclusions ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 * [ system ] ; Name Hexane [ molecules ] ; Compound #mols Hexane 125 ************************************************* Then I used the following comamnds: grompp -f em -c Hexane-Stack125.gro -p Hexane-Stack125-nrexcl19.top -o Hexane-Stack125_em >& output.grompp_em mdrun -s Hexane-Stack125_em -o Hexane-Stack125_em -c Hexane-Stack125_b4pr -v >& output.mdrun_em grompp -f md13 -c Hexane-Stack125_b4pr -p Hexane-Stack125-nrexcl19.top -o Hexane-Stack125_md >& output.grompp_md mdrun -rerun Hexane-Stack125_md.tpr.trr ------------------------------------------------------- Program mdrun, VERSION 4.0.7 Source code file: gmxfio.c, line: 737 Can not open file: topol.tpr ********************************************************************************************** Do I need to do this as: [exclusions] 1 2 1 3 1 4 ... 1 20 2 3 3 4 . . 3 20 . . since this involves tedious work I would like you to help me with first approach (nrexcl in moleculetype) and let me know what wrong is.. Thank you, moeed
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php