AMBER Archive (2006)

Subject: AMBER: AMBER : About the kinetic energy and temperature (GBSA model)

From: James W (c00jsw00_at_nchc.org.tw)
Date: Tue Mar 28 2006 - 20:00:46 CST

 Dear all,
       
 My system is SAMs (self assemble mileculars) , 120 units
       
 (ASP-CYS-CYS-CCCCCCCCCCCCCCCCC / unit ).
       
 And I used the GB model to simulated it , the input and output files are
       
 shown below .I am confused about the
       
 kinetic energy and temperature . I set the value of "temp0" equil to
       
 300.0 k .But when " NSTEP " is 700 ,
       
 I found that "TEMP(K) = 3107.84" . The temperature(nstep=700) is great
       
 than 300.0 K . Could you tell me
       
 what's wrong in my setting ?
       
 Thx
       
 Y.T
       
 wang
       
                                                                             
       
                                                                             
       
 Input file
       
 ____________________________________________________________________________________
 md
       
 &cntrl
       
 imin=0,
       
 ntc=2, ntf=2,
       
 cut=16.0, igb=2, saltcon=0.2, gbsa=1,
       
 ntpr=50,
       
 nstlim = 5000, dt=0.001,
       
 ntt=0, tempi=300.0, temp0=300.0,
       
 ntx=1, irest=0, ntb=0,
       
 nscm = 10,
       
 ntr=0,
       
 /
       
 END
       
 END
       
                                                                             
       
                                                                             
       
                                                                             
       
 output file
       
 ____________________________________________________________________________________
 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 300.30 PRESS = 0.0
       
 Etot = -1405.6547 EKtot = 932.7151 EPtot = -2338.3697
       
 BOND = 389.5255 ANGLE = 182.3471 DIHED = 515.4259
       
 1-4 NB = 147.9234 1-4 EEL = 2675.0993 VDWAALS = -351.1301
       
 EELEC = -5097.1779 EGB = -820.1518 RESTRAINT = 0.0000
       
 ESURF= 19.7689
       
 ------------------------------------------------------------------------------
     
                                                                             
       
 check COM velocity, temp: 0.015241 0.30(Removed)
       
 check COM velocity, temp: 0.000000 0.00(Removed)
       
 check COM velocity, temp: 0.000000 0.00(Removed)
       
 check COM velocity, temp: 0.000000 0.00(Removed)
       
 check COM velocity, temp: 0.000000 0.00(Removed)
       
                                                                             
       
 NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = 318.77 PRESS = 0.0
       
 Etot = -1405.4655 EKtot = 990.0818 EPtot = -2395.5473
       
 BOND = 307.5312 ANGLE = 594.5002 DIHED = 599.9923
       
 .............
       
 NSTEP = 700 TIME(PS) = 0.700 TEMP(K) = 3107.84 PRESS = 0.0
       
 Etot = 13564.6367 EKtot = 9652.8794 EPtot = 3911.7573
       
 BOND = 3513.7230 ANGLE = 3354.8521 DIHED = 1031.5089
       
 1-4 NB = 371.9003 1-4 EEL = 1603.3571 VDWAALS = -175.5535
       
 EELEC = -4548.6615 EGB = -1262.3852 RESTRAINT = 0.0000
       
 ESURF= 23.0162
       
 ------------------------------------------------------------------------------
     
                                                                             
       
 vlimit exceeded for step 700 ; vmax = 21.7882583078948926
       
 vlimit exceeded for step 701 ; vmax = 21.6897506373911106
       
                                                                             
       
                                                                             
       
                                                                             
        

--
National Center High-performance Computing (http://www.nchc.org.tw)

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