AMBER Archive (2009)

Subject: [AMBER] Re: AMBER: periodic bondary condition

From: Markus Kaukonen (markus.kaukonen_at_iki.fi)
Date: Fri Oct 16 2009 - 02:38:03 CDT


Dear Amber,

Is a covalent bond across a periodic boundary still impossible with Amber?

I'd like to make an infinitely long carbon nanotube...

I guess this type of simulations are becoming more and more common.

Terveisin, Markus

>Hi Wang,
>
>Do you mean you want to have some kind of infinite polymer? I.e. like a
>covalent surface that is then solvated in water? If so then unfortunately
>AMBER can't do this at present and you would have to modify the code
>yourself to do it. I believe that CHARMM can probably do it but I have never
>tried it.
>
>Good luck,
>Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of WANG,YING
> Sent: Friday, May 23, 2008 6:17 PM
> To: amber_at_scripps.edu
> Subject: AMBER: periodic bondary condition
>
> Hi, Dear Ambers,
>
> I solvate my specimen in explicit water, like TIP3P box. I let the
> buffer to be 8 angstrom. If I want to let some of the covalent
> bond across the periodic boundary condition, could anybody tell me
> how to acchieve it? Thanks very much in advance!!
>
>
>
> Best,
>
>
> Ying
> > To: amber_at_scripps.edu
> Subject: AMBER: periodic bondary condition

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--www=http://www.iki.fi/markus.kaukonen
--Markus.Kaukonen_at_iki.fi
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-- --www=http://www.iki.fi/markus.kaukonen --Markus.Kaukonen_at_iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) ---

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