Removed unnecessary static declarations for command-line parsing
For historical reasons command-line parsing needed static variables
when declaring the t_pargs structures, however modern compilers
do not need this anymore. Simultaneously, repeatedly calling a function
containing static variables may lead to irreproducible results.
The programs fixed here have no unit tests, however grompp and pdb2gmx
are tested in the regression tests, which pass.
Fixed uninitialized variable that turned up when not static anymore.
TODO: fix the same in analysis tools.
Part of #2113.
Change-Id: I1f67cc54362062289264b83078d3317f8e914faf