[gmx-users] g_mindist -pi option

[andrea spitaleri]

Hi Miguel,
that's it. Visualizing the system in vmd I see that at the point the two peptides are in two
different boxes.
I was almost sure that there were no interaction between two periodic images from the energy
profile. In fact, the energy profile (Coul and LJ) did not show any weird behaviour. Besides this,
it sounds very strange that the minimum distance goes from 3.0 nm to 0.17 nm and then up to 3.0 in 2
ps ...
Therefore vmd and energy profile seem to be consistent with a proper simulation (till now ..) :)
Thanks,

Regards

andrea

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.
> 
> 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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