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On 5/04/2012 1:58 PM, Acoot Brett wrote:
<blockquote
cite="mid:1333598314.12941.YahooMailNeo@web121805.mail.ne1.yahoo.com"
type="cite">
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255); font-family: times new roman,new york,times,serif;
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<div id="yiv2074674631">
<div>
<div style="color: rgb(0, 0, 0); font-family: times new
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<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
<a class="moz-txt-link-rfc2396E" href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations">"http://www.gromacs.org/Documentation/How-tos/Extending_Simulations"</a> ,
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
<a class="moz-txt-link-rfc2396E" href="http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File">"http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File"</a>,
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>
</div>
</blockquote>
<br>
No, they are different files, of different file types, containing
different information and used in different contexts. If you were to
swap those filenames between the two commands, neither would work.<br>
<br>
<blockquote
cite="mid:1333598314.12941.YahooMailNeo@web121805.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); 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> </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>
</div>
</blockquote>
<br>
The filename matters not. Whether it contains sensible raw material
for the trjconv operation given your objective matters.<br>
<br>
Mark<br>
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