[gmx-users] About Temperature Calculation

[Ane Xu]

Dear All:
    I am conducting simulation on carbon nanotubes, two nanotubes is
considered as a molecule and periodic boundary condition is applied, I
initiated the system with 300K by set gen-temp=300, while after
simulation, I found that the temperature at step0 is 500K, but
temperature of following steps calculated by g_energy is only about
160K, so I have two questions, I wish someone can help me to solve it.

1) Why the temperature of following steps is so much lower that of the
initial step.

2) How do g_energy calculate temperatures in such a system as mine,
i.e., structure A and B is connected by VDW interaction, they belong to
ONE molecule, but their COM may have oppsite motion. Does the velocity
of all atoms need to minus the COM velocity of the whole system or the
COM of their sub-structure seperatly (A or B).

     BTW, this mailist is so helpful to me, thanks a lot,.

Ane

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Ane Xu ( Xu ZhiPing )
Ph.D Candidate
Office: 3-405
Tel    : +86-10-627-83814
Department of Enginnering Mechanics
Tsinghua University
Beijing, CHINA, 100084
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