[gmx-users] g_mindist -pi option
machuque at itqb.unl.pt
Tue Jun 12 13:15:42 CEST 2007
At 08:00 AM 6/12/2007, you wrote:
>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.
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.
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