See <a href="http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions">http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions</a><br><br><div class="gmail_quote">On Jan 4, 2008 11:20 AM, tangxuan <<a href="mailto:tangxuan82@gmail.com">
tangxuan82@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Thanks for your detailed explanation. Sorry for my words and I wrote
<br>them in a hurry without careful check. In fact, I can not see a whole<br>protein in ref1.tpr and part of subunits are out of box.<br>I do not know if this can be called jump.<br><br>Tang<br><div><div></div><div class="Wj3C7c">
<br><br>Tsjerk Wassenaar wrote:<br>> Hi Tang,<br>><br>> The subunits have no contact each other obviously,<br>> without jump in them and I can not see an intact protein.<br>><br>><br>> Please be more clear and try to write full, correct sentences. I
<br>> suppose you mean that the subunits are separated at start, so there<br>> has been a jump in the setup stage.<br>><br>> However, the structure in the frames shows that there is a whole<br>> protein with jump.
<br>> Therefore, the structure in the tpr file is different from the<br>> structure<br>> in the first frame.<br>><br>><br>> So (one of the) subunits occasionally jump(s) back and make the<br>
> molecule "whole".<br>><br>> The simulation is 30ns long and I am trying to calculate the rmsf<br>> between 20ns and 30ns. I removed the jumps in whole<br>> simulation(trjconv<br>> -f .xtc(.trr) -s
ref1.tpr -pbc nojump) first and got the nojump xtc<br>> file between 20ns and 30ns.<br>><br>><br>> Assuming that ref1.tpr corresponds to your starting structure, which<br>> has the subunits separated, this means that you end up with a
<br>> trajectory which has the subunits separated consistently.<br>><br>><br>> 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.<br>><br>><br>> This reference may be of the correct complex (check it).<br>><br>> 2) used ref1.tpr and nojump trr file to get a tpr file at 20ns
<br>> ref20.tpr<br>> by tpbconv.<br>><br>><br>> And this will have the subunits separated.<br>><br>><br>> then "g_rmsf -f .xtc (nojump) -s ref20.tpr -res" is used to<br>> calculate
<br>> the rmsf.<br>><br>><br>> So the answer is in the structures (jump/nojump) and not in the way<br>> g_rmsf performs the fit and calculates the rmsf. Try to make this line<br>> of thinking your own and check the structures (references/selected
<br>> frames from trajectories) first whenever you encounter problems like<br>> this. This issue has also been covered before, and I recall having<br>> posted a message on this list regarding the correct use of references,
<br>> fitting and -pbc options using trjconv, which may be useful to you.<br>><br>> Cheers,<br>><br>> Tsjerk<br>><br>><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<br></div></div><div><div></div><div class="Wj3C7c">> ------------------------------------------------------------------------
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</a><br></div></div></blockquote></div><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