AMBER Archive (2002)

Subject: Re: Equilibration output Amber7

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Fri Nov 22 2002 - 08:42:02 CST

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