<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"> <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.<br>
<br>Turgay<br></span></font></font></pre>