-u option in benchmarking

[CatChenal]

The run script that has been used in the past is the following:

 #!/bin/bash
 step1.py --dry prot.pdb
 step2.py -d 8
 step3.py -d 8
 step4.py

 sleep 10

All the four steps have a common "-u" option (among others). As it is used to provide an alternate "MCCE folder" when benchmarking parameter sets, not using it is not an option.

Which is the preferable way to gather the "-u" option for the cli:

1. Just once to be used for all steps, i.e.:

   #!/bin/bash
   step1.py --dry prot.pdb -u <one_u>
   step2.py -d 8 -u <one_u>
   step3.py -d 8 -u <one_u>
   step4.py -u <one_u>
   
   sleep 10

2. For every steps, i.e.:

   #!/bin/bash
   step1.py --dry prot.pdb -u <u1>
   step2.py -d 8 -u <u2>
   step3.py -d 8 -u <u3>
   step4.py -u <u4>
   
   sleep 10

[CatChenal]

In this benchmarking context, the -u option will be mostly used for providing an alternate MCCE_HOME when benchmarking new atomic charges from various force fields.