[gmx-users] Problems with trajectories

Paulo Netz paulo.netz at gmail.com
Mon May 26 23:49:36 CEST 2014


Just a suggestion:

Try first to concatenate all the trajectory with trjcat and then
remove the periodicity effects with trjconv with the flag -pbc nojump.

Best regards

Paulo Netz

2014-05-26 16:39 GMT-03:00 Steve Seibold <stevesei at ymail.com>:

> I REALLY need some help here. I have tried for several days now and looked
> on line to fix the situation. My protein moves around and goes outside the
> simulation waterbox and my Zinc ions also frequently have bonds to protein
> of 40 angstroms are so.
> Here is one of the combinations I have tried so far to remove
> translational motion of protein and keep it in the center of the box:
> trajconv  -f pr13.trr ( traj. file containing the last 8 ps) -s pr1.tpr
> (containing the first pdb structure before any MD, but with waters etc)
> -pbc atoms (place all atoms into center of box) -center -boxcenter tric -o
> protein13.trr
> This  results in protein no longer separating into parts (pieces), but
> protein moves, still all over the box and outside of the box..and Zincs
> still have long bonds...
> Then, I use 'fit' as follows in an attempt to do a least squares fit of
> all trajectories (positions) back onto initial structure which is in center
> of box.....
> trajconv -s pr1.tpr -f protein13.trr (using the output from above) -fit
> progressive -o protein13A.trr
> This didn't help at all..
> I am really at a loss here on how to deal with this and could use some
> help..
> Steve
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