On 3/03/2012 5:08 PM, zhongjin wrote:
Dear gmx users,
It seems that I have found a strange temperature value after NVT
equilibrium for 200 ps. I simulate a CNT with two graphite sheets in
water box. I do not want to them to deform or change their shaps, So I
use a very large position restraint (1*10^6) to keep their shaps. The
temperature was set to 300 K, but after NVT equilibrium, the
tempertaure was 330K.
.mdp content
define = -DPOSRES_CNTGATE -DPOSRES_K -DPOSRES_CL
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 1
; Groups to couple separately
tc-grps = Other Water_and_ions
; Time constant (ps) and reference temperature (K)
tau-t = 0.1 0.1
ref-t = 300 300
results
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Temperature 331.548 2.6 10.3739 15.0042 (K)
T-Other 436.927 12 39.4112 67.2519 (K)
T-Water_and_ions 303.349 0.16 6.07417 1.02328 (K)
the Other, that is CNT and two graphite sheets temperature is very high!!!
Howerver when I freeze them, the temperture is OK
freezegrps = K CL Other
freezedim = Y Y Y Y Y Y Y Y Y
the results is
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Temperature 299.998 0.0034 4.84173 -0.0066645 (K)
T-Other 0 0 0 0 (K)
T-Water_and_ions 299.998 0.0034 4.84173 -0.0066645 (K)
So I should freeze them or use a small postion restraint to constaint
them, in order to get the correct temperture?
By introducing position restraints, you cause local heating because
there is a force whenever the positions deviate. Don't try to measure
local temperature until the model might make a sensible measurement,
i.e. after equilibration. That might mean several equilibration phases
where you relax your position restraints gradually.
The thin nature of the sheet and tube is also somewhat unfavorable for
the correct function of separate T-coupling groups. See manual 3.4.8,
particularly final subsection and ref therein.
Mark
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