<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div id="yiv2074674631"><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 id="yiv2074674631yui_3_2_0_17_133358881838643"><span id="yiv2074674631yui_3_2_0_17_133358881838679">Dear All,</span></div><div><span id="yiv2074674631yui_3_2_0_17_133358881838686"></span> </div><div><span id="yiv2074674631yui_3_2_0_17_1333588818386171">According to "http://www.gromacs.org/Documentation/How-tos/Extending_Simulations" , the commands for extending MD are:</span></div><div><span></span> </div><div><span></span> </div><div>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr<br>mdrun -s next.tpr -cpi previous.cpt</div><div> </div><div>But if you read
"http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File", it suggest for extension of MD, state.cpt should be used. But if we use state.cpt for extension, in</div><div> </div><div>"</div><div>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr<br>mdrun -s next.tpr -cpi previous.cpt</div><div>"</div><div> </div><div>the "previous" in previous.tpr in tpbconv will be conflicting with "previous" in previous.cpt in mdrun.</div><div> </div><div>In addition in command</div><div>"</div><div>trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact</div><div>"</div><div> </div><div>can we change md_0_1.xtc to traj.xtc?</div><div> </div><div>I am looking forward to getting a clarification from you.</div><div> </div><div>Cheers,</div><div> </div><div>Acoot<var id="yui-ie-cursor"></var></div><div><br> </div><div><br id="yiv2074674631yui_3_2_0_17_133358881838645"></div> <div
style="font-family: times new roman, new york, times, serif; font-size: 12pt;" id="yiv2074674631yui_3_2_0_17_133358881838649" class="yiv2074674631ms__id2257"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;" class="yiv2074674631ms__id2259"> <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="yiv2074674631hr yiv2074674631yui-non yiv2074674631yui-skip"></div> <b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Wednesday, 4 April 2012 6:56 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] the -extend function of the tpbconv command<br> </font>
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On 4/04/2012 6:24 PM, Acoot Brett wrote:
<blockquote type="cite">
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<div><span>Hi Justin and All,</span></div>
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<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;" class="yiv2074674631ms__id2270">-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;" class="yiv2074674631ms__id2271">-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>
</div>
</div>
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</blockquote>
<br>
Any change is enough to prevent appending. mdrun computed a checksum
when it wrote them, saved the checksums in the checkpoint file, and
demands that newly-computed ones match when attempting to append
later. Use only the original trajectory files when attempting to
append.<br>
<br>
Mark<br>
<br>
<blockquote type="cite">
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<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);" class="yiv2074674631ms__id2275">
<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="yiv2074674631yui-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>
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<div dir="ltr"> <font size="2" face="Arial"> <b><span style="font-weight: bold;">From:</span></b>
Justin A. Lemkul <a class="yiv2074674631moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu" rel="nofollow" target="_blank" ymailto="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Acoot Brett <a class="yiv2074674631moz-txt-link-rfc2396E" href="mailto:acootbrett@yahoo.com" rel="nofollow" target="_blank" ymailto="mailto:acootbrett@yahoo.com"><acootbrett@yahoo.com></a>;
Discussion list for GROMACS users
<a class="yiv2074674631moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <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>
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</div><br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel="nofollow" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" rel="nofollow" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="nofollow" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br> </div>
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