Search:
trjconv pbc cluster
on the gromacs mailing list and take a look at the first hit.
Basically, you need to find a frame that *does* work with -pbc cluster
and then make a new .tpr based on the clustered .gro and then run
trjconv -pbc mol. Just ensure that this frame is as close to the start
of your run as possible.
Chris.
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
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