[gmx-users] solvent temperature

[Justin A. Lemkul]

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:

http://www.gromacs.org/pipermail/gmx-users/2002-August/002244.html

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:

http://wiki.gromacs.org/index.php/thermostats

-Justin

> 
> Did I do something wrong, or has this to do with the constraints in the SCP
> topology?
> 
> Thank you in advance
> 
> Alberto Imparato
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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