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We tried to design PLUMED in such a manner that input/output is done consistently irrespectively of the file type. Most of the files written or read by PLUMED thus follow the very same conventions discussed below.
Whenever the RESTART option is used, all the files written by PLUMED are appended. This makes it easy to analyze results of simulations performed as a chain of several sub-runs. Notice that most of the PLUMED textual files have a header. The header is repeated at every restart. Additionally, several files have time in the first column. PLUMED just takes the value of the physical time from the MD engine. As such, you could have that time starts again from zero upon restart or not.
An exception from this behavior is given by files which are not growing as the simulation proceeds. For example, grids written with METAD with GRID_WFILE are overwritten by default during the simulation. As such, when restarting, there is no point in appending the file. Internally, PLUMED opens the file in append mode but then rewinds it every time a new grid is dumped.
Whenever the RESTART option is not used, PLUMED tries to write new files. If an old file is found in the way, PLUMED takes a backup named "bck.X.filename" where X is a progressive number. Notice that by default PLUMED only allows a maximum of 100 backup copies for a file. This behavior can be changed by setting the environment variable PLUMED_MAXBACKUP to the desired number of copies. E.g. export PLUMED_MAXBACKUP=10 will fail after 10 copies. PLUMED_MAXBACKUP=-1 will never fail - be careful since your disk might fill up quickly with this setting.
When running with multiple replicas (e.g., with GROMACS, -multi option) PLUMED adds the replica index as a suffix to all the files. The following command will thus print files named COLVAR.0, COLVAR.1, etc for the different replicas.
d: DISTANCE ATOMS=1,2 PRINT ARG=d FILE=COLVAR
(see also DISTANCE and PRINT).
When reading a file, PLUMED will try to add the suffix. If the file is not found, it will fall back to the name without suffix. The most important case is the reading of the plumed input file. If you provide a file for each replica (e.g. plumed.0.dat, plumed.1.dat, etc) you will be able to setup plumed differently on each replica. On the other hand, using a single plumed.dat will make all the replicas read the same file.
Notice that when PLUMED adds the replica suffix, it recognizes the file extension and add the suffix before the extension. Before PLUMED 2.2, the only recognized suffix was ".gz". Since 2.2, any suffix with length less or equal to five letters is recognized.
This means that using in a multireplica context an input such as
d: DISTANCE ATOMS=1,2 PRINT ARG=d FILE=COLVAR.gz METAD ARG=d FILE=test.HILLS SIGMA=0.1 HEIGHT=0.1
(see DISTANCE, PRINT, and METAD) PLUMED will write files named COLVAR.0.gz, COLVAR.1.gz, test.0.HILLS, test.1.HILLS, etc etc. This is useful since the preserved extension makes it easy to process the files later.
1.8.10 
