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

[hessb at mpip-mainz.mpg.de]

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
>> _______________________________________________
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-developers-request at gromacs.org.
>>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>