AMBER Archive (2007)

Subject: AMBER: abnormal high temperature during NPT ensembles MD

From: ebright HMS (amber.hms_at_gmail.com)
Date: Tue Feb 27 2007 - 17:13:29 CST

hi all :

I am simulating a small organic molecule (coumarin-like ) in explicit water
solvent by Amber 8. 1ns NVT ensemble equilibration run was first conducted
to make
sure the system equilibrate under constant volume. However, I observed
very abnormal high temperature (above 400K) in the followed NPT ensemble
production run although I set the temperature at 300K. It seems that the
system
is 'boiling' somehow. Can anybody give me some inputs why this happens ?
Thanks ! I listed the production run input and output below. Additionally, I
am
not able to set the cut-off at 10 or 12 since it always complains " Ewald
PARAMETER
RANGE CHECKING: out of legal range".

md3.in
------------------------
NPT production MD
 &cntrl
  imin = 0, irest = 1, ntx = 5,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 8, ntr = 0,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 100000, dt = 0.002,
  ntpr = 100, ntwx = 500, ntwr = 1000
 /
END

md3.out
-------------------------------------------------------------------------------------------------
check COM velocity, temp: 0.017613 0.47(Removed)

 NSTEP = 13000 TIME(PS) = 1226.000 TEMP(K) = 626.92 PRESS =
7428.4
 Etot = -1117.9956 EKtot = 1337.9965 EPtot = -
2455.9921
 BOND = 3.8632 ANGLE = 8.2509 DIHED =
4.8641
 1-4 NB = 6.6715 1-4 EEL = -32.0330 VDWAALS =
507.9005
 EELEC = -2955.5094 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 462.0735 VIRIAL = -1360.9398 VOLUME =
11366.1939
                                                    Density =
0.9452

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