About which files do you have to worry:
param.inc INCAR POSCAR POTCAR KPOINTSUse the makeparam utility to create the param.inc file. For a molecular dynamics PREC= Low is definitely sufficient. The INCAR file might be similar to
SYSTEM = Se PREC = Low ENCUT = 150 eV energy cutoff (opt) IALGO = 48 ; NELMIN = 3 LREAL = .TRUE. real space projections BMIX = 2.0 mixing parameter ISYM = 0 switch of symmetry EDIFF = 1E-3 Ionic Relaxation NSW = 100 number of steps for IOM NBLOCK = 1 ; KBLOCK = 100 SMASS = 2.0 Nose mass-parameter (am) POTIM = 3.00 time-step for ion-motion TEBEG = 573 temperature PC-function APACO = 10.0 distance for P.C. DOS related values: ISMEAR = 1 ; SIGMA = 0.1 EMIN = -20 ; EMAX = 5Use IALGO=48 (i.e. residual minimization) for large molecular dynamic runs. You should switch on the real space projection (LREAL=.TRUE.), and require at least 3 electronic iterations per ionic step (NELMIN=3).
Special consideration requires the parameter BMIX, usually the (quite heuristic) formula
gives a reasonable estimation for the optimal BMIX parameter. The remaining parameters can be looked up in the INCAR section (Sec. 7).
After doing one iteration it is only necessary to copy CONTCAR to POSCAR and restart VASP. Usually a shell script is used for this task. An example shell script can be found on the vamp account in the file vamp/scripts/iter.
If you are using time steps which are large in comparison
to the vibrational frequencies you should use the Verlet algorithm
instead of the predictor corrector algorithm. Normally the
predictor corrector algorithm improves the energy stability, but
because it is an "high order" algorithm it is also less stable
for large time steps. For instance we found that the Verlet algorithm
is superior for H 
O if 
fs (this means
that one period for bond stretching takes
approximately 10 time steps, the drift decreases by almost a factor
of 10 with the Verlet algorithm).
To use the Verlet algorithm change step.o in the makefile
to stepver.o. As a rule of thumb always use the Verlet algorithm
of you see strong oscillations in the total energy!