<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Dear Justin</span></div><div><span>many thanks for your helpful explanation. I did all the checks. the problem was related to the modified .xtc file. (the file created by running trjconv command on the original .xtc file). I do not have any idea that why this command created new .xtc file which was written only to for example 530 ps instead of 1000 ps !!!!</span></div><div><span>-------------</span></div><div><span>Thanks again</span></div><div><span>Regards</span></div><div><span>D.M</span></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, 18:01<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 9:28 AM, delara aghaie wrote:<br>> Dear Justin<br>> Thanks again. Ok I got it.<br>> Only there remains a question:<br>> you mean it is possible that the simulation has finished for 1 ns but the .xtc<br>> file does not have the information for whole frames or even it is possible for<br>> g_gyrate program to crash and give the non-compelete .xvg file?<br>><br><br>A large number of things are possible. You can use gmxcheck to verify the <br>integrity of the .xtc file, and inspect the .log file to make sure the <br>simulation was conducted as you expect it
to. If g_gyrate had crashed, it would <br>have been fairly obvious in the terminal.<br><br>-Justin<br><br>> Regards<br>> D.M<br>><br>> --------------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* delara aghaie <<a ymailto="mailto:d_aghaie@yahoo.com" href="mailto:d_aghaie@yahoo.com">d_aghaie@yahoo.com</a>>; Discussion list for GROMACS users<br>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Monday, 11 June 2012, 17:46<br>> *Subject:* Re: [gmx-users] radius of gyration<br>><br>><br>><br>> On 6/11/12 9:09 AM, delara aghaie wrote:<br>> > Dear Justin<br>> > My question can be related to both. Ok let me talk about the tutorial. The<br>> >
simulation has finished compeletly and log file and other outputs show the<br>> > completion of 1 ns simulation.<br>> ><br>> > this is part of gyrate.xvg file I see:<br>> > -------------<br>> > @ 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>> > ----<br>> > ---<br>> > 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>> > ---------------------------------------<br>> > This was the start and end of data reported in gyrate.xvg file.<br>> > all the outputs are written in files every 1000 steps (1000*0.002=2ps).<br>> > I expect to see in gyrate.xvg file, the last line for 500 which corresponds to<br>>
> the (500*2=1000ps)<br>> ><br>> > can you please explain the result for having lines till 530?<br>><br>> Your output file is not labeled according to frame number, it is labeled<br>> according to time and thus 530 corresponds to the time of 530 ps. If the file<br>> does indeed end there then either there is a corruption in the .xtc file, your<br>> simulation did not go to 1 ns, or g_gyrate exited prematurely. It's up to you<br>> to figure out what may have gone wrong. No one else can possibly know that.<br>><br>> > -----------<br>> > About plotting the graph if I know use the two first coloumns, I will not have<br>> > graph for Rg versus simulation time which I am interested in?<br>> ><br>><br>> That's precisely what you will have. Look at the data labels in the .xvg file<br>> and you will see what each data set
is.<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>><br>><br><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>
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