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