[gmx-users] g_mindist -pi option

[Tsjerk Wassenaar]

Hi Andrea,

You shouldn't fit before analysis involving PBC. Fitting changes the
orientation of the molecule with respect to the lattice. Image an
elongated molecule in a rectangular box, which rotates along its short
axis. Because of fitting, you'd miss it running into its own image...

Cheers,

Tsjerk

On 6/12/07, andrea spitaleri <spitaleri.andrea at hsr.it> wrote:
> Just to keep the post upgraded, I have tried:
> trjconv -pbc nojump -o test.xtc
> then
> trjconv -fit rot+trans -f test.xtc -o test1.xtc
> and then run g_mindist on test1.xtc.
> The results of -pi is more or less the same that I obtain using vmd program.
>
> Probably it might help other people with the same problem,
>
> Regards
>
> andrea
>
> Yang Ye wrote:
> > On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote:
> >> At 08:00 AM 6/12/2007, you wrote:
> >>> Hi again,
> >>> since I did not get answer I double checked my trr file. In case I
> >>> calculate the minimum distance of
> >>> the periodic image for each component of my complex, I get reasonable
> >>> value of it (3.0 and 2.9 nm),
> >>> whereas if I consider the whole system (protein) I get this strange
> >>> result of 0.17 nm.
> >>> Any clue?
> >>> thanks again
> >>> Regards
> >>
> >> Hi Andrea,
> >>
> >> When you have a multi-chain protein (or a protein + peptide) it can
> >> happen that when making protein whole (removing pbc) sometimes the two
> >> chains can be placed in two different adjacent boxes, so... when doing
> >> the "g_mindist -pi" setup, the closest distance is when they are
> >> together in the same box at a distance of ~1.7 Angstrom.
> >>
> >> Point 1 - This is an artifact, but it doesn't exclude the possibility
> >> that there are structures seeing their periodic images. As it was
> >> suggested by Mark Abraham, you should check these structures just to
> >> be sure.
> >>
> >> Point 2 - If someone knows how to trick trjconv -pbc in order to avoid
> >> doing this... it would be appreciated.
> > Yes. I got such "separated chain" trajectory with dsDNA as well. I have
> > a script to move them back manually frame per frame by comparing minimal
> > distance and real distance.
> >>
> >> Miguel
> >>
> >>
> >> ========================================
> >> Miguel Machuqueiro
> >> ITQB-Instituto de Tecnologia Química e Biológica
> >>     Universidade Nova de Lisboa
> >> Molecular Simulation Group - 6º Floor (Room 601)
> >> Av. da República, EAN, Apartado 127
> >> 2781-901 Oeiras, Portugal
> >> Tel. : +351 214469618 /Mobile: +351 96 7562285
> >> E-mail: machuque at itqb.unl.pt
> >> _________________________________________
> >>
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> --
> -------------------------------
> Andrea Spitaleri PhD
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> http://biomolecularnmr.ihsr.dom/
> -------------------------------
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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