<br><br><div class="gmail_quote">On Sat, May 19, 2012 at 3:21 PM, Turgay Cakmak <span dir="ltr"><<a href="mailto:turgaycakmak34@gmail.com" target="_blank">turgaycakmak34@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<p class="MsoNormal"><span style="font-family:"Times New Roman","serif"" lang="EN-US"><br></span></p><p class="MsoNormal"><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US">Hi Gromacs users,</span></font></p>
<p class="MsoNormal"><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US"><br></span></font></p>
<p class="MsoNormal"><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US">I have a question related to the extension of the
simulation.</span></font></p>
<p class="MsoNormal"><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US">I have done 10 ns simulation (several peptides in a
box). Now, I want to extend it 10ns more.</span></font></p><font size="4">
</font><p class="MsoNormal"><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US"><br></span></font></p><ul><li><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US">As far as I see from “Justin Lemkul’s Lysozyme in
water tutorial”, to extend simulation, following should be done. </span></font></li></ul><font size="4">
</font><p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><font size="4"><span style="font-family:"Times New Roman","serif""> grompp -f grompp.mdp -c first10ns.gro –t first10ns.cpt
-p topol.top -o second10ns.tpr</span></font></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><font size="4"><span style="font-family:"Times New Roman","serif""> </span></font></p><font size="4">
</font><ul><li><font size="4"><span style="font-family:"Times New Roman","serif"">But, another tutorial says that:</span></font></li></ul><font size="4">
</font>
<p class="MsoNormal"><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US"> tpbconv -f traj.trr -s topol.tpr -e ener.edr -o
tpxout.tpr –until $VALUE</span></font></p>
<p class="MsoNormal"><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US"> Where $VALUE = ps (e.g. if you wanted to extend a 2 ns
run to 5 ns, then $VALUE = 5000)</span></font></p><font size="4">
</font><pre><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US"></span></font></pre></blockquote><div>This option is fine. You don't need the .trr and .edr files if you supply a check-point file (.cpt) with -f option, to extend a simulation. </div>
<div> </div><div>-Anirban</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><pre><font size="4"><span style="font-family:"Times New Roman","serif"" lang="EN-US"> <br>
<font size="4">I am confused which one shuld have used. </font></span><font size="4"><span style="font-family:"Times New Roman","serif"">So, if someone could help me, I would be happy.<span class="HOEnZb"><font color="#888888"><br>
<br>Turgay<br></font></span></span></font></font></pre>
<br>--<br>
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