AMBER Archive (2002)

Subject: Re: large energy fluctration

From: eric hu (erichu_linux_at_yahoo.com)
Date: Fri Sep 20 2002 - 13:00:17 CDT

I don't think the energy is conserved since I'm using
NTT=1. But the total energy seems a little bit too big
to be anything useful. Here is the input and RMS
output:

cold start belly equil
 &cntrl
   IREST = 1, ibelly= 1,
   NTX = 5, TEMPI = 0.0,
   NTB = 0,
   NTT = 1, TEMP0 = 298.0, TAUTP = 1,
   NSTLIM= 150000, DT = .002,
   NTC = 3,
   NTF = 3,
   CUT =12.0, NSNB = 9999,
   NTPR = 20, NTWX = 20,
 &end
 -- belly = residues 18A from res 268 plus all H2O
RES 3 3
RES 6 6
RES 9 9
...

      R M S F L U C T U A T I O N S

 NSTEP = 150000 TIME(PS) = 310.000 TEMP(K) =
3.55 PRESS = 0.0
 Etot = 819.2380 EKtot = 27.8453 EPtot
    = 818.8379
 BOND = 0.0000 ANGLE = 31.5973 DIHED
    = 20.2013
 1-4 NB = 10.4871 1-4 EEL = 27.0086
VDWAALS = 33.6665
 EELEC = 820.6207 EHBOND = 0.0000
RESTRAINT = 0.0000

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

--- Carlos Simmerling <carlos.simmerling_at_sunysb.edu>
wrote:
> is the total energy conserved?
>
> ----- Original Message -----
> From: "eric hu" <erichu_linux_at_yahoo.com>
> To: "Carlos Simmerling"
> <carlos.simmerling_at_sunysb.edu>
> Sent: Saturday, September 14, 2002 2:31 PM
> Subject: Re: large energy fluctration
>
>
> > I changed the time step to 0.5fs and 1fs and they
> did
> > improve to some extent but are still not quite
> > satifying. I wonder if this is generally true for
> only
> > using shake on H atoms.
> >
> > Eric
> > --- Carlos Simmerling
> <carlos.simmerling_at_sunysb.edu>
> > wrote:
> > > 2fs time step with shake only on H atoms is
> > > a little large to expect good energy
> fluctuations
> > > and
> > > perfect average T. You might repeat with 1fs
> step
> > > and see if things improve. You probably
> > > don't need to run as long.
> > > carlos
> > >
> > > ----- Original Message -----
> > > From: "eric hu" <erichu_linux_at_yahoo.com>
> > > To: <amber_at_heimdal.compchem.ucsf.edu>
> > > Sent: Thursday, September 12, 2002 2:05 PM
> > > Subject: large energy fluctration
> > >
> > >
> > > > 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
> > > >
> > > >
> > > >
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