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

[chris.neale at utoronto.ca]

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
>
>