[gmx-users] g_mindist -pi option
leafyoung at yahoo.com
Tue Jun 12 13:55:38 CEST 2007
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
> 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 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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