[gmx-developers] trjconv -pbc whole appears to require whole molecules in the reference frame

[chris.neale at utoronto.ca]

Hello,

has anybody successfully utilized trjconv -pbc whole in gromacs 4.0.2?

I notice that in gmx_trjconv.c, bPBCWhole only appears to be utilized  
on line 788:
bRmPBC = bFit || bPBCWhole || bPBCcomRes || bPBCcomMol;

where the other options bPBCcomRes and bPBCcomMol have further  
processing starting at line 1234:
             if (bPBCcomRes) {
               put_residue_com_in_box(unitcell_enum,ecenter,
                                      natoms,atoms->atom,ePBC,fr.box,fr.x);
             }
             if (bPBCcomMol) {
               put_molecule_com_in_box(unitcell_enum,ecenter,
                                       &top.mols,
                                       natoms,atoms->atom,ePBC,fr.box,fr.x);
             }

If, indeed the bRmPBC is meant to make molecules whole, without any  
further processing, then it seems as if it must be done via line 940:

rm_pbc(&(top.idef),ePBC,atoms->nr,top_box,xp,xp);

and in this case, then I think that the trjconv -h output should be  
modified as follows:

Original:trjconv -pbc whole appears to require whole m
* whole only makes broken molecules whole.

New:
* whole only makes broken molecules whole if they are whole in the  
reference frame.

(although it would be nice if this requirement was eventually removed)

************

Thanks,
Chris.