AMBER Archive (2004)

Subject: AMBER: Temperature Regulation

From: Johnson Agbo (agboj_at_chem.unr.edu)
Date: Mon Jul 26 2004 - 23:40:44 CDT

Dear All;
We are running periodic boundary condition dynamics on 432 ice system
in a rectangular box of size 19.074, 19.074, 38.148. we are interested
in a constant temperature and constant pressure simulation. In order
to get a higher density of the ice to about 1.3 g/cm3, we set the
pressure to 10000 bars, the density came out as we expected but from
the output, we noticed that the temperature is far from the temperature
we want (temp0=50.0). Below are our input and output files.

molecular dynamics run
&cntrl
         imin=0, irest=1, ntx=5,
         ntt=1, temp0=50.0, tautp=2.,
         ntp=1, taup=1., ntave=1000,
         ntb=2, ntc=2, ntf=2,pres0=10000,
         nstlim=500000,
         ntwe=1000, ntwx=1000, ntpr=1000,
&end

     A V E R A G E S O V E R 500000 S T E P S

  NSTEP = 500000 TIME(PS) = 600.000 TEMP(K) = 80.40 PRESS =
9983.6
  Etot = -4942.7336 EKtot = 206.8291 EPtot =
-5149.5627
  BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
  1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1168.6964
  EELEC = -6318.2591 EHBOND = 0.0000 RESTRAINT =
0.0000
  EKCMT = 101.6708 VIRIAL = -2001.3074 VOLUME =
9759.0138
                                                 Density =
1.3248
  Ewald error estimate: 0.2385E-02
   
------------------------------------------------------------------------
------

       R M S F L U C T U A T I O N S

  NSTEP = 500000 TIME(PS) = 600.000 TEMP(K) = 5.21 PRESS =
331.0
  Etot = 25.3742 EKtot = 13.4066 EPtot =
14.5425
  BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
  1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
40.1570
  EELEC = 44.4396 EHBOND = 0.0000 RESTRAINT =
0.0000
  EKCMT = 6.9401 VIRIAL = 68.9753 VOLUME =
200.9400
                                                 Density =
0.0237
  Ewald error estimate: 0.1822E-02

We would appreciate if somebody could guide us out of this problem.

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