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 ENCUT = 150 eV ! energy cutoff (opt) IALGO = 48 ! RMM-DIIS algorithm for electrons LREAL = A ! evaluate projection operators in real space NELMIN = 4 ! do a minimum of four electronic steps BMIX = 2.0 ! mixing parameter MAXMIX = 50 ! keep dielectric function between ionic movements Ionic Relaxation ISYM = 0 ! switch of symmetry 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.Use IALGO=48 (RMM-DIIS for electrons) for large molecular dynamic runs. You should also evaluate the projection operators in real space (LREAL=A), and require at least 4 electronic iterations per ionic step (NELMIN = 4). For surface you might need to increase this value to NELMIN = 8.
Special consideration require the parameters BMIX and MAXMIX: it is usually desirable to use optimal mixing parameters for molecular dynamics simulations. This can be done by performing a few static calculations with varying AMIX and BMIX parameters and do determine the one leading to the fastest convergence. However in the latest version of VASP the dielectric function is reused when the ions are updated (an optimal AMIX and BMIX is no longer that important). The dielectric function is reused after ionic updates, if MAXMIX ist set. MAXMIX should be about three times as larger as the number of iterations required to converge the electronic wavefunctions in the first iteration.
After doing executing VASP once, it is only necessary to copy CONTCAR to POSCAR and to 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.