Hi Monika, Xavier,<br><br>You can't really judge a run from the rmsd ;)<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;">
g_rms and VMD should the exact same result. You might check the reference<br>frame you use and make sure you fit your protein using the same set of<br>atoms.<br><div class="Ih2E3d"></div></blockquote><div><br>I concur, and Xavier, you hit the spot with referring to the reference frame.
<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;"><div class="Ih2E3d">> 2. I have given two consecutive 3ns runs in continuation. first for 3ns,
<br>> then next again for 3ns. In latter, I used unconstrained-start=yes. When<br>> I am concatenating these xtc files, to get total of 6ns, and then doing<br>> g_rms, I am getting a dip at 3000 and there it seems to follow earlier
<br>> pattern of VMD.<br>> that 1 to 3000ps- values of rmsd decreases from 0.5 to 0.005 nm,<br>> then 3001 to 6000ps - values of rmsd increases from 0.0698 to 0.248 nm.<br><br></div>Check again your reference frame, and you may have made a mistake in your
<br>continuation run, I mean the way you actually continued it.<br><div class="Ih2E3d"></div></blockquote><div><br>So, what happens when you get a dip in the rmsd? The structure comes close to your reference structure. Or, the other way around, your reference structure seems to match the structure at the break of the trajectories. Thus, it seems that you have used the continuation run input file as the reference frame. I think that VMD only extracts the topology from the .tpr file and does the rmsd calculation with respect to the first set of coordinates in the trajectory.
<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">> In case of alone rmsd calculations, 3ns rmsd showed increasing
<br>> deviations from 0.0005 to 0.509 nm.<br>> 6ns run rmsd too showed increasing deviations from 0.00 to 0.248nm<br><br></div>This does not look like a regular continuation run. But again you<br>reference frame might be the problem.
<br><div class="Ih2E3d"></div></blockquote><div><br>Well, the rmsd tends to rise more during the first part of the simulation (relaxation effects, etc). So if you then take the run input file from the continuation run and use it to calculate the rmsd of the second part, it's likely that you'll see less of a rise in the rmsd.
<br></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;"><div class="Ih2E3d">> But when I am concatenating them, then the 3ns run showed deviations
<br>> down (different from its original) and 6ns showed up (similar to its<br>> original).<br><br></div>Then the reference frame is not the problem but the way you continued.<br>Do you fit your protein before the rmsd calculation?
<br><div class="Ih2E3d"></div></blockquote><div><br>Au contraire, the reference is the problem (or actually cause). <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d"><br>> I really dont know what is happening and why?? Where the things are<br>> going hay-ward??<br>></div></blockquote><div><br>Because of an inconsistent approach. Please think carefully about which reference file you use where. In these cases it's best to have a
start.tpr or something, which corresponds to the initial starting structure of your simulation, for analysis.<br><br>I hope it helps and best wishes for 2008 ;)<br><br></div></div>Tsjerk<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