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

[Mike Colvin]

Hi Mark,
    Thanks for that pointer.  I'm using Gromacs 4.0.3 and the drifting 
"Conserved En" value seems to occur in any NVT simulation using the 
Bussi, et al. thermostat.  To give a specific example, if one starts 
with the water example in the Gromacs distribution 
(gromacs-4.0.3/share/tutor/water) and changes the thermostat to 
"v-rescale", turns off the barostat, and comments out an obsolete 
option, and then runs it ("grompp" and "mdrun"), the resulting energy 
file will show a linearly increasing "Conserved En".  Here's the diff 
file between the new and original mdp files:

31c31
< ;bd-temp                  = 300
---
 > bd-temp                  = 300
123c123
< Tcoupl                   = v-rescale
---
 > Tcoupl                   = berendsen
130c130
< Pcoupl                   =
---
 > Pcoupl                   = berendsen

Thanks in advance for any guidance on this.

--Mike Colvin

>
>> 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
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