[email protected] 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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