[gmx-users] g_mindist after trjconv -fit give different results

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Dec 4 21:07:40 CET 2009

Hi Elad,

This has been mentioned several times before, in a different context.
But fitting only affects coordinates, and not the PBC. So after
fitting the coordinates and the PBC don't match any more and any
analysis requiring PBC, such as calculating minimal distances, will
give garbled results. Always do such things on untransformed



On Fri, Dec 4, 2009 at 7:43 PM,  <eladp at post.tau.ac.il> wrote:
> Hi all,
> I have a system of protein+water+ions.
> I measured the minimum distance between one of the ions to the protein.
> Afterwards I fitted the trajectory using g_trjconv -fit rot+trans
> Did the same mindist again and the graphs are not always identical.
> Any suggestions?
> I use gromacs 4.0.5 with an octahedron box.
> same problem happens when I do trjconv -fit rot but does not happen when
> -fit trans.
> In VMD I do see a difference in the position of the ion relative to the
> protein.
> Thanks.
> Elad P.
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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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