[gmx-users] g_rmsf fitting

[tangxuan]

Thanks for your detailed explanation. Sorry for my words and I wrote 
them in a hurry without careful check.  In fact, I can not see a whole 
protein in ref1.tpr and part of subunits are out of box.
I do not know if this can be called jump.

Tang


Tsjerk Wassenaar wrote:
> 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 "whole".
>
>     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.
>
> Cheers,
>
> Tsjerk
>
>
> -- 
> 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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