[gmx-users] solvent temperature
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 9 13:52:18 CET 2009
imparato at na.infn.it wrote:
> Dear users
> I have the following problem and was wondering if anyone can help me.
> I'm trying to set up some SDS + water simulations, with Beredsen
> temperature coupling
> tcoupl = Berendsen
> tc-grps = system
> tau_t = 0.1
> ref_t = 300
> when I use the rigid solvent topology
> #include "spc.itp"
> and try to sample the system temperature with
> g_traj -f full -s full -ot temp.xvg -xvgr
> if I consider separately the temperature of the SDS and the Solvent, the
> SDS has the correct temperature (around 300 K), the solvent has a wrong
> temperature (around 200 K).
> The system as a whole has a wrong temperature (around 210 K).
Sounds like the exact same issue reported here:
Use g_energy to extract temperatures.
> If I use the flexible solvent topology
> #include "flexspc.itp"
> then the temperature of the solvent is 300K, as expected.
> I have the same problem if I couple separately the SDS and the solvent to
> the termostat
> Tcoupl = Berendsen
> tc-grps = SDS SOL NA+ CL-
> tau_t = .1 .1 .1 .1
> ref_t = 300 300 300 300
Don't couple solvent and ions separately:
> Did I do something wrong, or has this to do with the constraints in the SCP
> Thank you in advance
> Alberto Imparato
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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