[gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 24 21:10:27 CET 2008

Suman Chakrabarty wrote:
> On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>> Tcoupl                   = v-rescale
>>> tc_grps                  = system
>>> tau_t                    = 0.1
>>> ref_t                    = 300.00
>> Maybe you want "Protein Non-Protein" instead of "system" here?  But that's
>> just general advice, without any knowledge of what's in your system.
> Just out of curiosity, how is it important to have different
> temperature coupling groups for the protein and the solvent? What are
> the problems one might face if a single group of "System" is used?
> That's what I am doing currently for a simulation of polymer in water.
> Is it suggested in general to have two different groups?

It's the classic "hot solvent-cold solute" problem that has been documented in 
the literature.  See for example: Lingenheil, et al. (2008) JCTC 4 (8): 1293-1306.

I made the mistake of using "system" myself for a while until it was pointed out 
to me on this list.


> Thanks,
> Suman.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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