Dear Gromacs users,
I am working with version 4.5.3, using the opls-aa forcefield in an implicit solvent, all-vs-all setting: pdb2gmx -ter -ff oplsaa -water none -f file.pdb I am energy-minimizing structures in 3 stages (steep, cg and l-bfgs). The last stage is the following: grompp -f em3.mdp -p topol.top -c em2.gro -t em2.trr -o em3.tpr -po em3.mdout.mdp mdrun -nice 0 -v -pd -deffnm em3 g_energy -s em3.tpr -f em3.edr -o em3.potential_energy.xvg where the mdp file is: ;;;;;;;;;;;;;;;;;;; em3.mdp ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; integrator = l-bfgs nsteps = 50000 implicit_solvent = GBSA gb_algorithm = Still sa_algorithm = Ace-approximation pbc = no rgbradii = 0 ns_type = simple nstlist = 0 rlist = 0 coulombtype = cut-off rcoulomb = 0 vdwtype = cut-off rvdw = 0 nstcalcenergy = 1 nstenergy = 1000 emtol = 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; The last line in the em3.potential_energy.xvg file should give the (potential) energy of the minimized structure em3.gro . I wish also to compute the potential energy of .gro files in general, not necessarily obtained from a simulation. For that, I prepared a .mdp file for a degenerate energy minimization, having 0 steps, designed just to give the status of the file: ;;;;;;;;;;;;;;;;;;; status.mdp ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; integrator = l-bfgs nsteps = 0 implicit_solvent = GBSA gb_algorithm = Still sa_algorithm = Ace-approximation pbc = no rgbradii = 0 ns_type = simple nstlist = 0 rlist = 0 coulombtype = cut-off rcoulomb = 0 vdwtype = cut-off rvdw = 0 nstcalcenergy = 1 nstenergy = 1 emtol = 0 ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; The only changes from the former .mdp file are in nsteps and nstenergy. However, when I run this potential energy status run on em3.gro itself, grompp -f status.mdp -p topol.top -c em3.gro -o status.tpr -po status.mdout.mdp mdrun -nice 0 -v -pd -deffnm status g_energy -s status.tpr -f status.edr -o status.potential_energy.xvg and look at the (single) energy line in status.potential_energy.xvg I find that the energy does not agree with the one obtained during minimization (it's higher by some tens of kJ/mol). What am I doing wrong? How should one reliably find the energy of a given .gro file? Moreover, when changing in status.mdp to integrator = steep, the results also change dramatically - why should the algorithm matter if no steps are performed and the initial structure is explored? Thanks, Ehud.
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