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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-SIZE: 14pt"><font face="Times New Roman"></font></span></p><span lang="EN-US" style="FONT-SIZE: 14pt"><font face="Times New Roman"><span lang="EN-US" style="mso-bidi-font-size: 10.5pt"><font face="Times New Roman">Hi all,</font></span></font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="mso-bidi-font-size: 10.5pt"><font face="Times New Roman">Recently, I run a carbon nanotube in vacuum using stochastic dynamics (Gromacs 3.3.1, integrator=sd) at 300K (ref_t=300.0) for 800 ps. The number of atoms of the CNT is about 5000, and the tube is left free to vibrate except for a few atoms are position restrained. When I set the tau_t=100, 0.2, 0.05, the actual simulation temperature fluctuates around an average value ~72K, 283K, 299K respectively.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="mso-bidi-font-size: 10.5pt"><font face="Times New Roman">I also run a peptide with about 110 atoms in vacuum using stochastic dynamics at 300K for 1 nanosecond. When I set the tau_t=100, 0.1, the actual simulation temperature fluctuates around an average value ~147K, 302K respectively.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="mso-bidi-font-size: 10.5pt"><font face="Times New Roman">So I want to know: Why different tau_t (with the same ref_t=300.0) can result in different temperature when the system is in vacuum? Can I perform the stochastic dynamic simulation in vacuum? If I can, can I used the tau_t=0.05, 0.1 for the CNT and peptide mentioned above respectively to couple the temperature of the system to 300K?</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="mso-bidi-font-size: 10.5pt"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>Thanks, </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="mso-bidi-font-size: 10.5pt"><font face="Times New Roman"><span style="mso-spacerun: yes"> </span>Xiu Peng.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="mso-bidi-font-size: 10.5pt"><font face="Times New Roman"> </font></span></p>
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