[gmx-users] g_rmsf fitting

[Tsjerk Wassenaar]

See http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions

On Jan 4, 2008 11:20 AM, tangxuan <tangxuan82 at gmail.com> wrote:

> 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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-- 
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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