[gmx-users] g_rmsf fitting

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 4 09:38:23 CET 2008

Hi Tang,

The subunits have no contact each other obviously,
> without jump in them and I can not see an intact protein.

Please be more clear and try to write full, correct sentences. I suppose you
mean that the subunits are separated at start, so there has been a jump in
the setup stage.

However, the structure in the frames  shows that there is a whole protein
> with jump.
> Therefore, the structure in the tpr file is different from the structure
> in the first frame.

So (one of the) subunits occasionally jump(s) back and make the molecule

The simulation is 30ns long and I am trying to calculate the rmsf
> between 20ns and 30ns. I removed the jumps in whole simulation(trjconv
> -f .xtc(.trr) -s ref1.tpr -pbc nojump) first and  got the nojump xtc
> file between 20ns and 30ns.

Assuming that ref1.tpr corresponds to your starting structure, which has the
subunits separated, this means that you end up with a trajectory which has
the subunits separated consistently.

> The main difference between is the tpr file
> at 20ns(ref20.tpr) i used and two ways I have used to get it:
> 1)  used ref1.tpr and original trr file to get a tpr file at 20ns
> ref20.tpr by tpbconv.

This reference may be of the correct complex (check it).

2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr
> by tpbconv.

And this will have the subunits separated.

> then "g_rmsf -f .xtc (nojump) -s ref20.tpr   -res" is used to calculate
> the rmsf.

So the answer is in the structures (jump/nojump) and not in the way g_rmsf
performs the fit and calculates the rmsf. Try to make this line of thinking
your own and check the structures (references/selected frames from
trajectories) first whenever you encounter problems like this. This issue
has also been covered before, and I recall having posted a message on this
list regarding the correct use of references, fitting and -pbc options using
trjconv, which may be useful to you.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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