AMBER Archive (2002)

Subject: Re: large energy fluctration

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Thu Sep 12 2002 - 13:50:09 CDT

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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