Dear all,
When I try to simulation with NVE ensemble, the total energy keeps decreasing. Geometry optimization and solvent equilibration are done before the NVE simulation. I follow the requirements provided in http://www.gromacs.org/Documentation/Terminology/NVE Would any one help me to figure out what was wrong with my settings? Millions of thanks and best wishes, Yun-an BTW: Please check the following for the .mdp file ;Run control: A leap-frog algorithm for integrating Newton's equations. integrator = md ;time step in femtoseconds dt = 0.001 ;number of steps nsteps = 10000000 ;No constraints constraints = none constraint_algorithm = shake shake_tol = 1e-08 ; group(s) for center of mass motion removal comm-grps = AA CCl4 ; frequency for center of mass motion removal nstcomm = 1000 ;frequency to write coordinates to output trajectory file nstxout = 1000 ;frequency to write velocities to output trajectory file nstvout = 1000 ;frequency to write energies to log file nstlog = 1000 ;frequency to write energies to energy file nstenergy = 1000 ;group(s) to write to energy file energygrps = System ;Frequency to update the neighbor list (and the long-range forces, ;when using twin-range cut-off's). nstlist = 10 ns_type = grid rlist = 1.5 ; Use periodic boundary conditions in all directions. pbc = xyz ;cut-off distance for the short-range neighbor list ;treatment of electrostatic interactions coulombtype = PME-switch fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 rcoulomb_switch = 1.0 rcoulomb = 1.2 ;treatment of van der waals interactions vdwtype = Switch rvdw-switch = 1.0 rvdw = 1.2 dispcorr = EnerPres ;Temperature coupling tcoupl = no ;Pressure coupling pcoupl = no ;Velocity generation gen_vel = no
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