Hello,<br><br>I am trying to get only interaction energies (vdw and electrostatics) between
hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in the system. I have added <u>exclusions section</u> at the end of top file to exclude all nonbonded interactions between atom 1 and all other 20 atoms. Unfortunately, I still have problem monitoring the breakdown of energies.<br>
<br>grompp -f em -c Hexane-Stack125.gro -p Hexane-Stack125-excl.top -o Hexane-Stack125_em >& output.grompp_em<br><br>mdrun -s Hexane-Stack125_em -o Hexane-Stack125_em -c Hexane-Stack125_b4pr -v >& output.mdrun_em<br>
<br>grompp -f md19 -c Hexane-Stack125_b4pr -p Hexane-Stack125-excl.top -o Hexane-Stack125_md >& output.grompp_md<br><br><b>mdrun -rerun -</b>s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr -c Hexane-Stack125_after_md -v >& output.mdrun_md<br>
<br>-------------------------------------------------------<br>Program g_energy, VERSION 4.0.7<br>Source code file: enxio.c, line: 283<br><br>Fatal error:<br>Energy file ener.edr not recognized, maybe different CPU?<br><br>
<br>*******em output:<br><br>Steepest Descents converged to Fmax < 1000 in 1 steps<br>Potential Energy = -1.06286703814635e+03<br>Maximum force = 2.02809790403662e+02 on atom 1183<br>Norm of force = 1.41349547097082e+02<br>
<br><br>********md output<br><br>Program mdrun, VERSION 4.0.7<br>Source code file: gmxfio.c, line: 737<br><br>Can not open file:<br>rerun.xtc<br><br><br><br>md.mdp <br><br><br>title = Hexane <br>cpp = /lib/cpp<br>
<br>; Run control<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 5000 ; total 1.0 ps.<br>nstcomm = 1 ; frequency for center of mass motion removal <br>
<br>; Output control<br>nstenergy = 10 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps<br>nstxout = 10 ; frequency to write coordinates/velocity/force to output trajectory file<br>
nstvout = 0<br>nstfout = 10<br>nstlog = 10 ; frequency to write energies to log file<br>energygrps = Hexane Hexane<br><br>; Neighbor searching<br>nstlist = 10 ; neighborlist will be updated at least every 10 steps <br>
;ns_type = grid<br><br>; Electrostatics/VdW<br>coulombtype = PME <br>vdw-type = cut-off<br>; Cut-offs<br>rlist = 1.0<br>rcoulomb = 1.0<br>
rvdw = 1.0<br><br>; Temperature coupling Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = HEX ;sol<br>tau_t = 0.1 ;0.1<br>
ref_t = 300 ;300<br><br>; Pressure coupling: Pressure coupling is not on<br>Pcoupl = no<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>
<br>; Velocity generation Generate velocites is on at 300 K. Manual p155<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br>; Bonds<br>constraints = all-bonds<br>
constraint-algorithm= lincs<br><br><b>; Energy group exclusions<br>eneegygrp_excl = HEX </b><br><br><br>pbc=xyz<br><br><br><br><br>/*********************topology file:<br><br>;<br>; File 'Hexane-PRODRG.top' was generated<br>
; By user: moeed (500)<br>; On host: moeed-desktop<br>; At date: Tue May 11 09:31:28 2010<br>;<br>; This is your topology file<br>; "Everything He Lacks, He Makes Up In Denial" (Offspring)<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>[ system ]<br>
; Name<br>Hexane<br><br>[ molecules ]<br>; Compound #mols<br>Hexane 125<br><br><b>[ exclusions ]<br><br>1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20</b><br><br><br>
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