Suman Chakrabarty wrote:
On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <[EMAIL PROTECTED]> 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.
-Justin
Thanks,
Suman.
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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