Running Molecular Dynamics

Presumably you have an appropriately created geo file as a starting structure.

In the control file, make sure that imetho is set to 0.

In the MD parameters section, most of the default values work well. Here are the key ones and what they mean.
         0.250  tstep  - the MD time step; there should be no need to change this.
       300.00  mdtemp  - temperature of the MD simulation
       100.00  tdamp1  - the temperature damp (usually 25-40% of mdtemp)
      400000  nmdit  - number of MD iterations, e.g. 400000 x 0.250 = 100000 fs or 100 ps or 0.1 ns
             020  iout1 - how often output is written to fort.71, fort.73, fort.75
             100  iout2 - how often the coordinates are saved and appended to xmolout
           5000  iout6 - how often to write out molsav.xxxx files

To run with variable temperature or variable volume, you can use the tregime.in or vregime.in files. If present, they are used. If not, only the specifications in the control file are used.

Important Output files:
The final structure at the end of the minimization is fort.90
The final velocities are written to moldyn.vel
Copies of the intermediate velocities are written to molsav.xxxx (can be deleted if the run went smoothly)
The concatenated geometry trajectory is written to xmolout
Total energy (KE, PE) and temperature trajectory written to fort.71
Breakdown of PE terms trajectory written to fort.73
A trajectory grouping molecular formulas together is written to molfra.out

To continue the dynamics,
(1) copy fort.90 (the latest structure) into geo,
(2) copy moldyn.vel into vels
(3) copy xmolout (and maybe fort.71 and fort.73 and molfra.out if needed) to some other filename so you save the previous trajectory some place,

then run the executable.