RE: [AMBER] help

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 30 Jan 2009 05:42:33 -0800

Hi Momo,

> My FINAL RESULTS look =
>
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 10000 4.1105E+02 3.0132E+00 1.7689E+01 H117 14
>
> BOND = 2.6696 ANGLE = 17.0783 DIHED =
> 158.3704
> VDWAALS = -37.1515 EEL = -631.0683 HBOND =
> 0.0000
> 1-4 VDW = 32.3588 1-4 EEL = 868.7910 RESTRAINT =
> 0.0000
>
> Is it an obligation to obtain a negative ENERGY else in what kind of
> simulation we must have a negative energy ???

No. This has been discussed on the list several times before. E.g.:
http://archive.ambermd.org/200803/0088.html

The origin in classical MD simulations is essentially arbitrary and changes
between different molecules. Take a look at equation and you should see that
it a positive energy is perfectly reasonable.

Good luck,
Ross


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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Sun Feb 01 2009 - 01:08:58 PST
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