<div dir="ltr"><div>Marcella,</div><div><br></div><div>Are you referring to the cp2k section <a href="https://manual.cp2k.org/cp2k-8_1-branch/CP2K_INPUT/MOTION/MD/PRINT/ROTATIONAL_INFO.html" id="m_-4553906892312800677gmail-CP2K_INPUT/MOTION/MD/PRINT/ROTATIONAL_INFO.html" style="text-decoration-line:none;font-family:Meiryo" target="_blank">ROTATIONAL_INFO</a> ?</div><div>If so, I was afraid I didn't consider the section.</div><div><br></div><div>Here is my simulation output on calculation of degrees of freedom.</div><div><br></div> DOF| Calculation of degrees of freedom<br> DOF| Number of atoms 100<br> DOF| Number of intramolecular constraints 0<br> DOF| Number of intermolecular constraints 0<br> DOF| Invariants (translations + rotations) 3<br> DOF| Degrees of freedom 297<div><br></div><div>The number of the translational and rotational degrees of freedom seem to be 3×(100-1) = 297, 0×(100-0) = 0.</div><div><br></div><div>I calculated the temperature considering the number of translational degrees of freedom (3) '<span style="color:rgb(80,0,80)">1/2*m*v^2 = 3/2*kb*T'</span>.</div><div>However I didn't consider the number of rotational degrees of freedom because it seemed to be 0.</div><div><br></div><div>Kind regards</div><div>Matsuo</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2022年6月11日(土) 16:21 Marcella Iannuzzi <<a href="mailto:marci.akira@gmail.com" target="_blank">marci.akira@gmail.com</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">What about the translational and rotational degrees of freedom?<div>Kind regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Saturday, June 11, 2022 at 4:59:33 AM UTC+2 mto wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="auto">Hi Marcella,</div><div dir="auto"><br></div><div>Thank you for your response.</div><div><br></div><div>Yes, I believe I have.</div><div>I calculated the temperature of the system by using the following method.</div><div><ol><li>Temperatures of each atom at 0th step were calculated with 1/2*m*v^2 = 3/2*kb*T, here the value of 'm' is mass in atomic mass units (amu).<br>mass: 28.0855 (Si), 15.9994 (O), 12.0107 (C)<br>amu = 1.660538782E-27 kg<br>mSi = amu*28.0855 kg, mO = amu*15.9994 kg, mC = amu*12.0107 kg<br>v^2 = (vx^2 + vy^2 + vz^2)*10^10 (m/s)^2<br>kb = 1.3806504E-23 m^2*kg*s^-2*K^-1<br></li><li>0th step temperature (T_all) is calculated <br>I have 32 Si, 64 O and 4 C, so I calculated the temperature of each individual atom and determined the average T<br>T_Si_k = mSi*v^2/(3*kb)<br>T_O_k =
mO*v^2/(3*kb)<br>T_C_k =
mC*v^2/(3*kb) (k represents the ID of the atom.)<br>T_all = (T_Si_1 + T_Si_2 + ... +T_Si_32 + T_O_1 + T_O_2 + ... + T_O_64 + T_C_1 + T_C_2 + ... T_C_4) / (32 + 64 + 4)</li></ol></div><div>Is this what you were referring to when you suggested looking at the degrees of freedom?</div><div dir="auto"><br></div><div dir="auto">Regards</div><div dir="auto">Matsuo</div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2022年6月10日(金) 1:04 Marcella Iannuzzi <<a rel="nofollow">marci...@gmail.com</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"></blockquote></div></div></div><div dir="ltr"><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><br></div>Hi <div><br></div><div>Are you sure that you considered the correct number of degrees of freedom?</div><div>Regards</div><div>Marcella</div><div><br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, June 9, 2022 at 6:09:06 AM UTC+2 mto wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear cp2k users,<div><br></div><div>I wanted to conduct a comparison and performed ab initio molecular dynamics (MD) simulations with an imposed initial temperature of 300 K. I then calculated the temperature from the velocities at the 0th step, but this value was 297K, which does not match with the temperature I set. I calculated the latter temperature (297K) from '<a href="http://0step_velocities.xyz" rel="nofollow" target="_blank">0step_velocities.xyz</a>' which is attached on this message. Both of them must be the same because the 0th step velocities are determined by the initial temperature. (The equation I used: 1/2m*v^2 = 3/2kb*T )</div><div>Does anyone know why there is a difference in temperatures? </div><div><br></div><div>Thank you in advance,</div><div>Matsuo</div></blockquote></div>
<p></p></blockquote></div></div></div><div dir="ltr"><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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