<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div>Dear Justin</div><div>My question can be related to both. Ok let me talk about the tutorial. The simulation has finished compeletly and log file and other outputs show the completion of 1 ns simulation.</div><div><br></div><div>this is part of gyrate.xvg file I see:</div><div>-------------</div><div>@ s0 legend "Rg"<br>@ s1 legend "RgX"<br>@ s2 legend "RgY"<br>@ s3 legend "RgZ"<br> 0 1.40391 1.20269 1.02309 1.20363<br> 2 1.41596 1.21322 1.03459 1.21146<br> 4
1.41283 1.21881 1.02271 1.20861<br> 6 1.41882 1.21595 1.03424 1.2157<br> 8 1.4139 1.20694 1.03791 1.21006<br> 10 1.42295 1.21367 1.03899 1.22356<br> 12 1.42184 1.20803 1.0391 1.22646<br>----</div><div>---</div><div> 518 1.41756
1.20547 1.04411 1.21475<br> 520 1.42478 1.21366 1.04952 1.21882<br> 522 1.41129 1.20451 1.04001 1.20458<br> 524 1.42205 1.20918 1.04929 1.21711<br> 526 1.41778 1.20381 1.04779 1.21375<br> 528 1.41853 1.20465 1.06006
1.20398<br> 530 1.42129 1.20401 1.05779 1.21307<br> 288,8 Bot<br>---------------------------------------</div><div>This was the start and end of data reported in gyrate.xvg file.</div><div>all the outputs are written in files every 1000 steps (1000*0.002=2ps).</div><div>I expect to see in gyrate.xvg file, the last line for 500 which corresponds to the (500*2=1000ps)</div><div><br></div><div>can you please explain the
result for having lines till 530?</div><div>-----------</div><div>About plotting the graph if I know use the two first coloumns, I will not have graph for Rg versus simulation time which I am interested in?</div><div><br></div><div>Thanks for your time</div><div>Regards</div><div>D.M<br></div><div><br></div><div><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> delara aghaie <d_aghaie@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Monday, 11 June 2012, 17:21<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] radius
of gyration<br> </font> </div> <br><br><br>On 6/11/12 8:40 AM, delara aghaie wrote:<br>> Dear Justin.<br>> Thanks for your explanation.<br>> ............................................................<br>> In lyzozyme tutorial the radius of gyration has been plooted against simulation<br>> time (there 1000 ps).<br>> When I plot the same graph, the horizontal axis is up to 500 (The number of<br>> frames for data calculation).<br>> Although, the gyrate.xvg file has gyration data for these 500 frames, how can I<br>> tell gnuplot to plot gyration versus simulation time (1000 ps)?<br>> <br><br>Are you talking about the tutorial or your own data? If you are talking about the tutorial, then the run should have been for 1 ns. If there are fewer frames, then either the .mdp file was changed to specify less time or the simulation stopped prematurely.<br><br>If you're talking about your own data, I have no way to know
what was expected. You can't plot more frames than are present. I don't use gnuplot so I can't offer you any advice as to how you can manipulate the way the data are displayed.<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul, Ph.D.<br>Research Scientist<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br><br><br> </div> </div> </div></body></html>