Equilibration output Amber7 from Fredrick Robin Devadoss on 2002-11-22 (Amber Archive Nov 2002)

From: Fredrick Robin Devadoss <fredrick_at_mbu.iisc.ernet.in>
Date: Fri 22 Nov 2002 15:12:32 +0530 (IST)

Dear amber users,
while running an equilibration, i got the following in the output
file........... check COM velocity, temp: 0.000002 0.00(Removed)
it comes in between every 50 steps.......... like this.........

HERE IS THE OUTPUT:

check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)

NSTEP = 50 TIME(PS) = 0.050 TEMP(K) = 6.33 PRESS =
1764.8
Etot = 4513.9746 EKtot = 168.5182 EPtot =
4345.4564
BOND = 14.0843 ANGLE = 103.8661 DIHED =
387.9850
1-4 NB = 176.4341 1-4 EEL = -10.8820 VDWAALS =
-3307.9063
EELEC = 6978.7228 EHBOND = 0.0000 RESTRAINT =
3.1523
EAMBER (non-restraint) = 4342.3042
EKCMT = 123.2608 VIRIAL = -6858.4457 VOLUME =
183229.3353
                                                Density =
0.7435
Ewald error estimate: 0.5609E+00

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

check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)
check COM velocity, temp: 0.000002 0.00(Removed)

Like this, it's keep on going upto NSTEP=1000...........

Can anyone explain me why it is coming like this?
my input file is as follows............

Equilibration run for heating the system
&cntrl
   imin = 0, ntx = 1, ntrx = 1, ntxo = 1, ntpr = 50,
   irest = 0, ntwr = 1000, ntwx = 1000,
   ntwv = 1000, ntwe = 1000, ntf = 2, ntc = 2,
   cut = 8.0, igb = 0, scee = 1.2, scnb = 2.0,
   nsnb = 25, dielc = 78.5, ntr = 1,
   nstlim = 1000, nscm = 1, t = 0, dt = 0.001,
   temp0 = 20.0, tempi = 0.0,
   heat = 0.0, ntb = 2, ntt = 1, tautp = 0.10,
   ntp = 1, pres0 = 1.0, comp = 44.6, taup = 0.2,
   tol = 0.0001,
&end
&ewald
   nfft1 = 64, nfft2 = 64, nfft3 = 64, order = 4,
   ew_type = 0, dsum_tol = 0.00001, nbflag = 0,
   eedmeth = 5,
&end
group no 1
10
RES 1 24
END
END

Can anyone explain me why it is coming like this?

thanks in advance

regards
fredrick.

-- 
From cuigl_at_morita.chem.sunysb.edu 22 Nov 2002 09:42:02 -0500
Message-id: <1037976122.10467.4.camel.poblano.bio.sunysb.edu>
Date: 22 Nov 2002 09:42:02 -0500
From: Guanglei Cui <cuigl_at_morita.chem.sunysb.edu>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: Re: Equilibration output Amber7
In-Reply-to: <Pine.LNX.4.44.0211221459190.1470-100000.mbu.iisc.ernet.in>
Hi, 
    COM stands for center of mass. Because you specified nscm = 1, which
means removing translation and rotation of COM is turned on, you had all
the COM messages. But I noticed that your EWALD error is quite big.
On Fri, 2002-11-22 at 04:42, Fredrick Robin Devadoss wrote:
> Dear amber users,
> while running an equilibration, i got the following in the output 
> file........... check COM velocity, temp:    0.000002   0.00(Removed)
> it comes in between every 50 steps.......... like this.........
> 
> HERE IS THE OUTPUT:
> 
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)
> 
>  NSTEP =     50 TIME(PS) =     0.050  TEMP(K) =     6.33  PRESS =  
> 1764.8
>  Etot   =    4513.9746  EKtot   =     168.5182  EPtot      =    
> 4345.4564
>  BOND   =      14.0843  ANGLE   =     103.8661  DIHED      =     
> 387.9850
>  1-4 NB =     176.4341  1-4 EEL =     -10.8820  VDWAALS    =   
> -3307.9063
>  EELEC  =    6978.7228  EHBOND  =       0.0000  RESTRAINT  =       
> 3.1523
>  EAMBER (non-restraint)  =    4342.3042
>  EKCMT  =     123.2608  VIRIAL  =   -6858.4457  VOLUME     =  
> 183229.3353
>                                                 Density    =       
> 0.7435
>  Ewald error estimate:   0.5609E+00
>  
> ------------------------------------------------------------------------------
> 
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)           
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)
> check COM velocity, temp:        0.000002     0.00(Removed)
> 
> Like this, it's keep on going upto NSTEP=1000...........
> 
> Can anyone explain me why it is coming like this?
> my input file is as follows............
> 
> 
> Equilibration run for heating the system
>  &cntrl
>    imin = 0, ntx = 1, ntrx = 1, ntxo = 1, ntpr = 50,
>    irest = 0, ntwr = 1000, ntwx = 1000,
>    ntwv = 1000, ntwe = 1000, ntf = 2, ntc = 2,
>    cut = 8.0, igb = 0, scee = 1.2, scnb = 2.0,
>    nsnb = 25, dielc = 78.5, ntr = 1,
>    nstlim = 1000, nscm = 1, t = 0, dt = 0.001,
>    temp0 = 20.0, tempi = 0.0,
>    heat = 0.0, ntb = 2, ntt = 1, tautp = 0.10,
>    ntp = 1, pres0 = 1.0, comp = 44.6, taup = 0.2,
>    tol = 0.0001,
>  &end
>  &ewald
>    nfft1 = 64, nfft2 = 64, nfft3 = 64, order = 4,
>    ew_type = 0, dsum_tol = 0.00001, nbflag = 0,
>    eedmeth = 5,
>  &end
> group no 1
> 10
> RES 1 24
> END
> END
> 
> Can anyone explain me why it is coming like this?
> 
> thanks in advance
> 
> regards
> fredrick.
-- 
Guanglei Cui <cuigl_at_morita.chem.sunysb.edu>
SUNY at Stony Brook

Received on Fri Nov 22 2002 - 01:42:32 PST