[gmx-users] Relationship between temperature, molecular velocity, and intramolecular potential
chungsh at umich.edu
Thu Nov 20 21:52:08 CET 2008
Recently, I got weird results from my simulations. My NVT system
contains about 300 molecules, which are looks similar to the C60
fullerenes but a little bit modified.
I simulated them with two conditions:
1) constrained bonds
2) harmonic bonds
The problem is this:
When I measured the average 'molecular' velocity, case 1 is much faster
than case 2.
I thought the molecular translational energy is independent to the
molecular internal energy. But this result is completely opposite to
this reasoning. It seems like internal vibration increase the system
temperature and, as a result, it lowers the molecular translational
energy of case 2 when it compare to that of case 1.
Their 'atomistic' average velocity are same (therefore, their measured
temperatures are the same because, to my knowledge, GROMACS uses
atomistic vel. for temperature) but 'molecular velocity' is not same. Is
this right conclusion?
I'm asking this because my previous thought was they were independent
and the molecular velocities of case 1 and case 2 were the same.
I tried both nose-hoover and berendensen and got the same results.
Thank you in advance,
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