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

[Suman Chakrabarty]

On Tue, Nov 25, 2008 at 1:40 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.


Thank you very much! I was not aware of this! Saves me a lot of
mistakes of future! :)


--Suman.