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What is the difference between the amount of memory used for applications and the PBS ?

The amount of memory specified on PBS is the environment to process the jobs.
For instance, we specify like this;
'select=1:mpiprocs=4:ncpus=4:mem=30gb'
This means that the job uses 30 GB memory with 4 MPI processes. In short, each process uses roughly 7.5 GB.
On the other hand, we sometimes specify the amount of memory for the application as well.

1.gaussian
At the beginning of the input data, the amount of memory is specified as %men.
On gaussian, specification of the memory to be used is important 
and calculation may be unable to be performed due to insufficient memory depending on the case. 
The algorithm used may be changed by the specification of a memory, the keyword which restricts the size of .rwf file on a hard disk(mentioned later),  or the specification of MaxDisk 
You have to change the amount of memory and hard disk size, considering  the size of calculation scheme,  the basic function to be used and the calculation technique.
In order to use limited computer resources effectively, it is important not to perform rash calculation.
In addition, It is necessary to acquire enough experience.
 Example)
  (gaussian) %mem=512MB  -->  (PBS) select=1:mem=8gb

2. ABAQUS
In TSUBAME, Available memory is 1GB by default.
When modify it, please execute abaqus command specified with memory option.

$ abaqus job=Job-name memory="10gb"