[gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

[Visvaldas K.]

I thought I was sure -pbc cluster will work, but it doesn't :( trjconv get's stuck on an infinite loop while calculating center of mass.

In an index.ndx I created a new group which I called CLUSTER, as Mark suggested (I used make_ndx), then I ran trjconv:

trjconv -f 1Y2Elig_em.trr -s 1Y2Elig_em.tpr -o tmp.pdb -b 120 -e 125 -pbc cluster -n index.ndx

What I get is an infinite loop:

COM:    2.784     1.968     3.409  iter = 1  Isq = 1840514.500
COM:    4.175     5.905     3.409  iter = 2  Isq = 230100.828 
COM:    2.784     1.968     3.409  iter = 3  Isq = 1840514.500
COM:    4.175     5.905     3.409  iter = 4  Isq = 230100.828 
COM:    2.784     1.968     3.409  iter = 5  Isq = 1840514.500
COM:    4.175     5.905     3.409  iter = 6  Isq = 230100.828 
COM:    2.784     1.968     3.409  iter = 7  Isq = 1840514.500
COM:    4.175     5.905     3.409  iter = 8  Isq = 230100.828 
COM:    2.784     1.968     3.409  iter = 9  Isq = 1840514.500
COM:    4.175     5.905     3.409  iter = 10  Isq = 230100.828
...
which goes on forever...

What am I doing wrong? (Should I attach the files?)
Thank you for your time!
Vis


> Dear GROMACS users and gurus,
> 
> I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been driving me crazy.  I have a protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces "clustered" compactly for some postprocessing,  using trjconv for conversion of trr/xtc into PDB format:
> 
> "-pbc mol" option of trjconv: metal ions are far from the rest of the protein.
> -pbc nojump or -pbc whole: inhibitor far from the protein, metals are fine.
> -pbc atom or -pbc res: couple of residues are disattached from the protein; metals and inhibitor are fine.
> -pbc cluster: doesn't work (irrelevant?)

-pbc cluster should work with a suitable index group of 
protein+metal+inhibitor - that's what it is for.

Once that's done, you may want to re-run trjconv to apply other effects. 
Two-pass processing is often necessary.

> Also -center and -boxcenter don't seem to help...
> Can anybody suggest some tricks? I used octahedral box for my runs.

"don't seem to help" also doesn't help. We can't guess what it was about 
your inputs and outputs that was contrary to your hopes :-)

Mark