<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Justin and All,</span></div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div id="yiv2064845834"><div><div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><div><span></span> </div><div><span>The on-line document on "<font style="background-color: rgb(255, 255, 0);">Exten</font>ding Simulations" writes,</span></div><div><span></span> </div><div><span>"You might want to use the <span style="font-family: courier new, courier, monospace;">-append</span> option of <a title="Documentation/Gromacs_Utilities/mdrun" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun" rel="nofollow"
target="_blank"><font color="#0066cc">mdrun</font></a> to append the new output to the old files. Note that this will only work when the old output files have not been modified by the user. Appending is the default behavior as of version 4.5."</span></div><div><span></span> </div><div><span>We can see "Appending is the default behavior as of version 4.5",
and what I use is version 4.5. Thus for mdrun, even without mention "<span style="font-family: courier new, courier, monospace;">-append</span> " appending should be automatically done.</span></div><div><span></span> </div><div><span>In addition, after the old output files were created, I only use the "trjconv" to process them, and I did not modify them.</span></div><div><span></span> </div><div><span>Thus the reason why the extended part output files were not automatically appended to my original old outputfiles according to what I have done (tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt)<var id="yiv2064845834yui-ie-cursor"></var> is still unclear.</span></div><div><span></span> </div><div><span>Will you please give an
explaination?</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot</span></div><div><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="yiv2064845834hr"></div> <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> Acoot Brett <acootbrett@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Wednesday, 4 April 2012 10:36 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] the
-extend function of the tpbconv command<br> </font> </div> <br><br><br>Acoot Brett wrote:<br>> Dear All,<br>> I have completed a 1ns production MD. Then I intended to extend it for another 1 ns.<br>> I use command<br>> "tpbconv -s previous.tpr -extend timetoextendby -o next.tpr<br>> mdrun -s next.tpr -cpi previous.cpt"<br>> I think the results will be automatically attended to previous md_0_1.tpr and md_0_1_noPBC.xtc.<br>> <br><br>Only if you then run mdrun -append and the files are appended. tpbconv doesn't do any of this for you, it just creates a new run input file capable of running a longer simulation. The fact that you have a file called "md_0_1_noPBC.xtc" seems like you've manipulated it in some way, so you shouldn't (and likely can't) append to it. You should append to your original files.<br><br>> Then I use "g_rms -s
md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" to get the rmsd.xvg file. Then I use "xmgrace -nxy potential.xvg" to display it. However I find for the curve the x-axis is from 0 ns to 1 ns, not from 0 ns to 2 ns.<br>> <br><br>If you haven't run a new simulation, you'll only have the data that already exists.<br><br>> The definition of "-extend" of the command "tpbconv" is "Extend runtime by this amount (ps)". Thus the commands I used are correct.<br>> <br><br>You haven't shown us your actual tpbconv command, so there's no way to verify that. In any case, tpbconv doesn't actually extend the simulation, mdrun does.<br><br>> Will you please tell me how to process for the extension MD so that the curve of the rmsd.xvg (and all the other xvg files) will have x-axis from the 0 to the 2 ns (2 ns is the total MD time, including the 1 ns extended part)?<br>> <br><br>There are two steps here:<br><br><a
href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4" rel="nofollow" target="_blank">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4</a><br><br>You need to do both.<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<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" rel="nofollow" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br> </div> </div> </div></div></div><meta content="on" http-equiv="x-dns-prefetch-control"><br><br> </div> </div> </div></body></html>