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<p>Dear gmx'ers,</p>
<p><br></p>
<p>I am somewhat confused relating temperatures and kinetic energies in gromacs output.</p>
<p>I simulate NVE system of N0 rigid molecules in vacuo, 'comm_mode' is set to 'None'. When I check the output 'Kinetic En.' and 'Temperature', the relation between them (see Eq. (3.13) of Manual) corresponds to 6*N0 degrees of freedom, that's OK.</p>
<p>Then the system is divided into two groups with N1 and N0-N1 molecules. While reruning the simulation (with 'energygrps' option), the energies of both groups are written to energy file, and the output includes also 'Temp_group1' and 'Temp_group2'. My wish is to obtain separate kinetic energies of the groups. I try to calculate them using for group degrees of freedom 6*N1 and 6*(N0-N1) values, resp. The problem is that the sum of instantaneous group kinetic energies is not equal to full 'Kinetic En.'! I could suppose that it is due to some relative motion of the groups, but the difference in energies through the simulation may be both positive and negative.</p>
<p><br></p>
<p>What is the real source of this difference?</p>
<p><br></p>
<p>Thanks in advance,</p>
<p><span class=rvts6>-- </span></p>
<p><span class=rvts6>Regards,</span></p>
<p><span class=rvts6> Dmitri </span><a class=rvts7 href="mailto:ddubov@ngs.ru">mailto:ddubov@ngs.ru</a></p>
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