[gmx-developers] Question about Conserved Energy value in NVT simulations with new thermostat.

[Mark Abraham]

Mike Colvin wrote:
> Hi All,
>    First, thanks to the developers for quickly incorporating Bussi, et 
> al.'s new velocity rescaling thermostat. The thermostat works great, but 
> I have a question about the "Conserved En" term reported, which so far 
> as I could glean from the source is the same as the Bussi's effective 
> energy (H hat) defined in eq. 15 of his paper.  However, for some NVT 
> test simulations that seem otherwise very well behaved, the Conserved 
> Energy changes steadily over the simulation which I wouldn't expect for 
> simulations with sufficiently small time steps. For a liquid argon test 
> case (T=303.9, dens=1.485 gm/cm3) this value drops exactly linearly in 
> time with a slope that is exactly proportional to the timestep (tested 
> at 2fs, 1fs, and .5 fs).  For an SPC/E water (at STP) this value drifts 
> upward during the simulation with a slope that is roughly proportional 
> to the square root of the timestep (ts=.25, .5, 1, and 2fs).  Anyway, I 
> was curious if anyone else had noticed this phenomena and whether I'm 
> misinterpreting what this term is.  (And please let me know whether this 
> or the gmx-user list is the best place for a question like this.)   

I can't help you on the point of your question, but if there's a real 
issue involved, at the very least people will want to know your GROMACS 
version, the contents of your .mdp file and mdrun command line. You may 
get a helpful response more quickly if you provide that information.

Mark