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

[hessb at mpip-mainz.mpg.de]

Hi,

Molecules are made whole by the rm_pbc call.
The two calls you mention put (parts of) molecules
in the box, they do not make them whole.

I think (but I have not tested it) that -pbc whole
should work in 4.0.2.

Berk

> 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.
>
>
>
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