Dear Mark and ALL, I am trying to calculate the conserved energy (H-tilde) in Bussi's stochastic velocity rescale algorithm (jcp,2007). In previous maillist, Mark had mentioned that the conserved En. in ener file is the H in bussi's paper (http://permalink.gmane.org/gmane.science.biology.gromacs.user/63005). According to the eq. 15 in Bussi's paper, we just need to get the time integration of dK if we have had the H. I carefully checked the coupling.c file, and noticed a variable - therm_integral[i] in the fucntion vrescale_tcoupl(). The therm_integral[i]-= Ek_new - Ek. It seems like an accumulation of the -dK. If it realy is the sum of -dK, the problem could become simple. What we need to do is just like this: H-tilde=H-Tau-t* therm_integral[i].? Is that right? I really need your help. Any suggestion is valuable.
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