[gmx-users] g_mindist -pi option

[andrea spitaleri]

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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> 
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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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