I am trying to calculate the mean temp of coarse-grained cholesterol from two commands and I get two different outputs. As I have used martini 2 cholesterol for my paper, I have to be sure that my systems dont have the problem about the cholesterol temp ( doi:10.1021/acs.jpcb.1c03665)
However, when I use gmx trjconv, I get T~150! (my coupling temp was 323). When I use “gmx energy”, I get T= 321 K.
Can someone tell me which one is the correct one? (Hopefully the second one) and why this happens?
My guess is that your cholesterol model uses constraints. gmx traj does not know about constraints and therefore reports a lower temperature in such cases. You can manually correct the temperature by multiplying it by the factor: 3 * #atoms_in_molecule / (3 * #atoms_in_molecule - #constraints).
Just to be sure I got it right, if I have 8 atoms in a molecule and 5 bonding constraints, the factor is calculated like this:
= 8/3 ~ 2.6
or
= 24/19~ 1.2
??
Thanks.
When I get cholesterol temperature with the energy file, the T is 321 K which is good enough. But, when I calculate it by velocities the mean T is 133 K. Even by multiplying by (24/19), it does not get the correct T. Would you please tell me what is the problem?
I found this in this paper (https://pubs.acs.org/doi/10.1021/acs.jpcb.1c03665) which gives the answer:
"the eight CG beads of CHOL would result in 3N = 24 degrees of freedom. However, the three massless virtual particles with 9 degrees of freedom do not contribute to the kinetic energy, and in addition, five constraints are present in the CHOL topology. Thus, in fact, the CHOL molecules only have 10 degrees of freedom
so the factor will be (24/10) = 2.4 and T is 133*2.4 ~320