<span>Hi</span> Tang,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">The subunits have no contact each other obviously,
<br>without jump in them and I can not see an intact protein. </blockquote><div><br>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.
<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">However, the structure in the frames shows that there is a whole protein with jump.
<br>Therefore, the structure in the tpr file is different from the structure<br>in the first frame.<br></blockquote><div><br>So (one of the) subunits occasionally jump(s) back and make the molecule "whole".<br><br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">The simulation is 30ns long and I am trying to calculate the rmsf<br>between 20ns and 30ns. I removed the jumps in whole simulation(trjconv
<br>-f .xtc(.trr) -s ref1.tpr -pbc nojump) first and got the nojump xtc<br>file between 20ns and 30ns. </blockquote><div><br>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.
<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">The main difference between is the tpr file<br>at 20ns(ref20.tpr) i used and two ways I have used to get it:
<br>1) used ref1.tpr and original trr file to get a tpr file at 20ns<br>ref20.tpr by tpbconv.</blockquote><div><br>This reference may be of the correct complex (check it).<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr<br>by tpbconv.</blockquote><div><br>And this will have the subunits separated. </div><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
then "g_rmsf -f .xtc (nojump) -s ref20.tpr -res" is used to calculate<br>the rmsf.<br></blockquote><div> <br>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.
<br><br></div></div>Cheers,<br><br>Tsjerk<br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands
<br>P: +31-30-2539931 <br>F: +31-30-2537623