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On 3/03/2012 5:08 PM, zhongjin wrote:
<blockquote
cite="mid:1330754882.32906.YahooMailClassic@web15608.mail.cnb.yahoo.com"
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<div>Dear gmx users,</div>
<div> </div>
<div> 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.</div>
<div> </div>
<div>.mdp content</div>
<div>define = -DPOSRES_CNTGATE
-DPOSRES_K -DPOSRES_CL</div>
<div>; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>
; Temperature coupling <br>
tcoupl = v-rescale<br>
nsttcouple = -1<br>
nh-chain-length = 1<br>
; Groups to couple separately<br>
tc-grps = Other Water_and_ions<br>
; Time constant (ps) and reference temperature (K)<br>
tau-t = 0.1 0.1<br>
ref-t = 300 300</div>
<div> </div>
<div>results</div>
<div>Energy Average Err.Est.
RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Temperature 331.548 2.6
10.3739 15.0042 (K)<br>
T-Other 436.927 12
39.4112 67.2519 (K)<br>
T-Water_and_ions 303.349 0.16
6.07417 1.02328 (K)</div>
<div> </div>
<div>the Other, that is CNT and two graphite sheets
temperature is very high!!!</div>
<div> </div>
<div>Howerver when I freeze them, the temperture is OK</div>
<div> </div>
<div>freezegrps = K CL Other<br>
freezedim = Y Y Y Y Y Y Y Y Y</div>
<div> </div>
<div>the results is</div>
<div><br>
Energy Average Err.Est.
RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Temperature 299.998 0.0034
4.84173 -0.0066645 (K)<br>
T-Other 0 0
0 0 (K)<br>
T-Water_and_ions 299.998 0.0034
4.84173 -0.0066645 (K)</div>
<div> </div>
<div>So I should freeze them or use a small postion
restraint to constaint them, in order to get the correct
temperture?</div>
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<br>
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.<br>
<br>
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.<br>
<br>
Mark<br>
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