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

[Mike Colvin]

Hi Berk,
    Thanks for the suggestion--I'll check if cut-offs are causing this 
drift.

--Mike Colvin

hessb at mpip-mainz.mpg.de wrote:
> Hi,
>
> This sounds exactly like cut-off effects.
> You have to be very careful with several mdp options
> to get good energy conservation.
> If you want this or not depends on your goals.
>
> For good energy conservation you have to use, for instance,
> vdwtype=shift with a buffer region and coulombtype=pme.
>
> Berk
>
>   
>> 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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>>     
>
>
>
>   
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