AMBER Archive (2002)

Subject: large energy fluctration

From: eric hu (erichu_linux_at_yahoo.com)
Date: Thu Sep 12 2002 - 13:05:10 CDT

I tried a 1ns md belly run according to the biotin and
dna tutorial. It seems to me that the total energy
fluctrates a lot. The rms keeps increasing. Here are
my input and part of the output results. Also it is a
little suspicious that the average temperature is not
298.

Eric

  belly equil
 &cntrl
   IREST = 1, ibelly= 1,
   NTX = 5,
   NTB = 0,
   NTT = 1, TEMP0 = 298.0, TAUTP = 1,
   DTEMP = 2.0, NTP = 0,
   NSTLIM= 500000,dt=0.002
   NTC = 2,
   NTF = 2,
   CUT =8.0
   NTPR = 200, NTWX = 200,
 &end
 -- belly = residues 15A res 268 plus all H2O
RES 6 6
RES 21 21
RES 25 25
RES 30 41
RES 43 45
RES 47 48
...

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

 NSTEP = 500000 TIME(PS) = 1010.000 TEMP(K) =
302.84 PRESS = 0.0
 Etot = -3444.7308 EKtot = 2130.0419 EPtot
    = -5574.7727
 BOND = 459.6763 ANGLE = 1259.5963 DIHED
    = 1669.7771
 1-4 NB = 630.6526 1-4 EEL = 7220.6871
VDWAALS = -1128.1817
 EELEC = -15686.9804 EHBOND = 0.0000
RESTRAINT = 0.0000

------------------------------------------------------------------------------

      R M S F L U C T U A T I O N S

 NSTEP = 500000 TIME(PS) = 1010.000 TEMP(K) =
3.96 PRESS = 0.0
 Etot = 790.0900 EKtot = 27.8453 EPtot
    = 790.1593
 BOND = 17.7467 ANGLE = 26.0593 DIHED
    = 16.9349
 1-4 NB = 10.4300 1-4 EEL = 26.8816
VDWAALS = 27.4592
 EELEC = 792.3181 EHBOND = 0.0000
RESTRAINT = 0.0000

__________________________________________________
Do you Yahoo!?
Yahoo! News - Today's headlines
http://news.yahoo.com