Hi Aneesh,
The absolute value of energy in classical MD simulations is not in itself
relevant. The origin is effectively arbitrary. It is relative differences
that are of interest.
I see nothing wrong with the values you provide below.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of aneesh cna
> Sent: Tuesday, May 05, 2009 10:58 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] High energy during minimization
>
> Dear David and Bill,
> Thanks for your kind reply. I can able rectify the problem with leap
> and
> structure is looking fine now, but still the system have high positive
> energy during the simulation. I can't able to figure out the exact
> problem.
> A part of the output file is given below. Please have a look and help
> me
>
> ***********************************************************************
> ********************
>
> A V E R A G E S O V E R 100000 S T E P S
>
> NSTEP = 100000 TIME(PS) = 700.000 TEMP(K) = 299.91 PRESS =
> 199.9
> Etot = 26758.9414 EKtot = 13635.8590 EPtot =
> 13123.0823
> BOND = 1939.7948 ANGLE = 7047.8861 DIHED =
> 3285.9498
> 1-4 NB = 1611.8557 1-4 EEL = 58661.2231 VDWAALS =
> -19144.1023
> EELEC = -40279.5248 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 5957.0400 VIRIAL = 3338.8033 VOLUME =
> 606689.6355
> Density =
> 0.9532
> Ewald error estimate: 0.2723E-04
> ***********************************************************************
> ***************************
>
> Thanks in advance
> Aneesh
>
> On Sun, May 3, 2009 at 11:30 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > Unless you actually have three-atom or four-atom rings in your
> > structure..
> >
> > If you look at it in xleap you will see all the bonds that leap
> > knows about.
> >
> > Bill
> >
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Received on Wed May 20 2009 - 14:50:21 PDT
