On Mon, Jan 10, 2011, subrata paul wrote:
>
> I am simulating a system containing only water in amber 10
> I made the system using following command..
>
> 1. xleap -s -f leaprc.GLYCAM_06
> 2. x=copy SPC
> 3. solvatebox x SPCBOX 12.0
> 4. saveamberparm x x.prmtop x.inpcrd
>
> Is this correct way for making the system?????
Sounds fine. (A single "?" is sufficient.)
>
> trajin xxxxx.mdcrd
> radial OW_OH .1 10 :WAT.O :WAT.H*
>
> after ploting in xmgrace I got a sharp peak of hight 25 at .98.
>
> Is this peak for bonded Hydrogen atom ????
Yes.
...dac
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Received on Mon Jan 10 2011 - 07:00:02 PST
