Hello Justin,<br><br>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:<br>
<br><br>checking input for internal consistency...<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp<br>
Generated 332520 of the 332520 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>Excluding 19 bonded neighbours molecule type 'Hexane'<br>
<br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.7<br>Source code file: smalloc.c, line: 147<br><br>Fatal error:<br>Not enough memory. Failed to calloc 78089438 elements of size 8 for s<br>
(called from file topexcl.c, line 161)<br>-------------------------------------------------------<br><br>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<br>
<br><br>; Include forcefield parameters<br>#include "ffoplsaa.itp"<br><br>[ moleculetype ]<br>; Name nrexcl<br>Hexane 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>
1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot -0.18<br> 2 opls_140 1 HEX H11 1 0.06 1.008 ; qtot -0.12<br> 3 opls_140 1 HEX H12 1 0.06 1.008 ; qtot -0.06<br>
4 opls_140 1 HEX H13 1 0.06 1.008 ; qtot 0<br> 5 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot -0.12<br> 6 opls_140 1 HEX H21 2 0.06 1.008 ; qtot -0.06<br>
7 opls_140 1 HEX H22 2 0.06 1.008 ; qtot 0<br> 8 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot -0.12<br> 9 opls_140 1 HEX H31 3 0.06 1.008 ; qtot -0.06<br>
10 opls_140 1 HEX H32 3 0.06 1.008 ; qtot 0<br> 11 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot -0.12<br> 12 opls_140 1 HEX H41 4 0.06 1.008 ; qtot -0.06<br>
13 opls_140 1 HEX H42 4 0.06 1.008 ; qtot 0<br> 14 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot -0.12<br> 15 opls_140 1 HEX H51 5 0.06 1.008 ; qtot -0.06<br>
16 opls_140 1 HEX H52 5 0.06 1.008 ; qtot 0<br> 17 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot -0.18<br> 18 opls_140 1 HEX H61 6 0.06 1.008 ; qtot -0.12<br>
19 opls_140 1 HEX H62 6 0.06 1.008 ; qtot -0.06<br> 20 opls_140 1 HEX H63 6 0.06 1.008 ; qtot 0<br><br>[ bonds ]<br>; ai aj funct c0 c1 c2 c3<br>
1 2 1 <br> 1 3 1 <br> 1 4 1 <br> 1 5 1 <br> 5 6 1 <br> 5 7 1 <br> 5 8 1 <br> 8 9 1 <br> 8 10 1 <br> 8 11 1 <br> 11 12 1 <br>
11 13 1 <br> 11 14 1 <br> 14 15 1 <br> 14 16 1 <br> 14 17 1 <br> 17 18 1 <br> 17 19 1 <br> 17 20 1 <br><br>[ pairs ]<br>; ai aj funct c0 c1 c2 c3<br>
1 9 1 <br> 1 10 1 <br> 1 11 1 <br> 2 6 1 <br> 2 7 1 <br> 2 8 1 <br> 3 6 1 <br> 3 7 1 <br> 3 8 1 <br> 4 6 1 <br> 4 7 1 <br>
4 8 1 <br> 5 12 1 <br> 5 13 1 <br> 5 14 1 <br> 6 9 1 <br> 6 10 1 <br> 6 11 1 <br> 7 9 1 <br> 7 10 1 <br> 7 11 1 <br> 8 15 1 <br>
8 16 1 <br> 8 17 1 <br> 9 12 1 <br> 9 13 1 <br> 9 14 1 <br> 10 12 1 <br> 10 13 1 <br> 10 14 1 <br> 11 18 1 <br> 11 19 1 <br> 11 20 1 <br>
12 15 1 <br> 12 16 1 <br> 12 17 1 <br> 13 15 1 <br> 13 16 1 <br> 13 17 1 <br> 15 18 1 <br> 15 19 1 <br> 15 20 1 <br> 16 18 1 <br> 16 19 1 <br>
16 20 1 <br><br>[ angles ]<br>; ai aj ak funct c0 c1 c2 c3<br> 2 1 3 1 <br> 2 1 4 1 <br> 2 1 5 1 <br> 3 1 4 1 <br>
3 1 5 1 <br> 4 1 5 1 <br> 1 5 6 1 <br> 1 5 7 1 <br> 1 5 8 1 <br> 6 5 7 1 <br> 6 5 8 1 <br> 7 5 8 1 <br>
5 8 9 1 <br> 5 8 10 1 <br> 5 8 11 1 <br> 9 8 10 1 <br> 9 8 11 1 <br> 10 8 11 1 <br> 8 11 12 1 <br> 8 11 13 1 <br>
8 11 14 1 <br> 12 11 13 1 <br> 12 11 14 1 <br> 13 11 14 1 <br> 11 14 15 1 <br> 11 14 16 1 <br> 11 14 17 1 <br> 15 14 16 1 <br>
15 14 17 1 <br> 16 14 17 1 <br> 14 17 18 1 <br> 14 17 19 1 <br> 14 17 20 1 <br> 18 17 19 1 <br> 18 17 20 1 <br> 19 17 20 1 <br>
<br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 c5<br> 2 1 5 6 3 <br> 2 1 5 7 3 <br> 2 1 5 8 3 <br>
3 1 5 6 3 <br> 3 1 5 7 3 <br> 3 1 5 8 3 <br> 4 1 5 6 3 <br> 4 1 5 7 3 <br> 4 1 5 8 3 <br> 1 5 8 9 3 <br>
1 5 8 10 3 <br> 1 5 8 11 3 <br> 6 5 8 9 3 <br> 6 5 8 10 3 <br> 6 5 8 11 3 <br> 7 5 8 9 3 <br> 7 5 8 10 3 <br>
7 5 8 11 3 <br> 5 8 11 12 3 <br> 5 8 11 13 3 <br> 5 8 11 14 3 <br> 9 8 11 12 3 <br> 9 8 11 13 3 <br> 9 8 11 14 3 <br>
10 8 11 12 3 <br> 10 8 11 13 3 <br> 10 8 11 14 3 <br> 8 11 14 15 3 <br> 8 11 14 16 3 <br> 8 11 14 17 3 <br> 12 11 14 15 3 <br>
12 11 14 16 3 <br> 12 11 14 17 3 <br> 13 11 14 15 3 <br> 13 11 14 16 3 <br> 13 11 14 17 3 <br> 11 14 17 18 3 <br> 11 14 17 19 3 <br>
11 14 17 20 3 <br> 15 14 17 18 3 <br> 15 14 17 19 3 <br> 15 14 17 20 3 <br> 16 14 17 18 3 <br> 16 14 17 19 3 <br> 16 14 17 20 3 <br>
<br>; Include Position restraint file<br>;#ifdef POSRES<br>;#include "posre.itp"<br>;#endif<br><br>; Include water topology<br>;#include "spc.itp"<br><br>;#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>
;[ position_restraints ]<br>; i funct fcx fcy fcz<br> ; 1 1 1000 1000 1000<br>;#endif<br><br>; Include generic topology for ions<br>;#include "ions.itp"<br><br><b>[ exclusions ]<br>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20<br></b><br>[ system ]<br>; Name<br>Hexane<br><br>[ molecules ]<br>; Compound #mols<br>Hexane 125<br><br>*************************************************<br>
<br><br>Then I used the following comamnds:<br><br>grompp -f em -c Hexane-Stack125.gro -p Hexane-Stack125-nrexcl19.top -o Hexane-Stack125_em >& output.grompp_em<br><br><br>mdrun -s Hexane-Stack125_em -o Hexane-Stack125_em -c Hexane-Stack125_b4pr -v >& output.mdrun_em<br>
<br><br> grompp -f md13 -c Hexane-Stack125_b4pr -p Hexane-Stack125-nrexcl19.top -o Hexane-Stack125_md >& output.grompp_md<br><br><br>mdrun -rerun Hexane-Stack125_md.tpr.trr <br><br><br>-------------------------------------------------------<br>
Program mdrun, VERSION 4.0.7<br>Source code file: gmxfio.c, line: 737<br><br>Can not open file:<br>topol.tpr<br><br><br>**********************************************************************************************<br><br>
<br><br>Do I need to do this as:<br>
<br>
[exclusions]<br>
1 2<br>
1 3<br>
1 4<br>
...<br>
1 20<br>
2 3<br>
3 4<br>
.<br>
.<br>
3 20<br>
.<br>
<br>
.<br><br><br>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..<br>
<br><br>Thank you,<br>moeed<br><br><br><br><br>