[gmx-users] g_mindist after trjconv -fit give different results
tsjerkw at gmail.com
Fri Dec 4 21:07:40 CET 2009
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
> Elad P.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Tsjerk A. Wassenaar, Ph.D.
More information about the gromacs.org_gmx-users