[gmx-users] g_rmsf fitting

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 4 09:36:47 CET 2008

tangxuan wrote:
> Hi Tsjerk,
> Yes, you are right. My protein has multiple subunits.  I have a original 
> tpr file ref1.tpr which is the input to start the simulation. I have 
> checked the protein structure
> in this tpr file. The subunits have no contact each other obviously, 
> without jump in them and I can not see an intact protein. 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. 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. 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.
> 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr 
> by tpbconv.
> then "g_rmsf -f .xtc (nojump) -s ref20.tpr   -res" is used to calculate 
> the rmsf.
> I take out part of the result below and the results are from two methods 
> for same subunit.

What happens whan you overlay the two reference structures using 
g_confrms? Is it high RMSD?
Both reference structures and trajectories should be jump-free.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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