[gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Mon Dec 28 17:22:37 CET 2009
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.
> 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!
>> 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
>> "-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 :-)
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