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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of WANG,YING
> Sent: Friday, May 23, 2008 6:17 PM
> To: amber.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.scripps.edu
> Subject: AMBER: periodic bondary condition
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--
--www=http://www.iki.fi/markus.kaukonen
--Markus.Kaukonen.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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Received on Fri Oct 16 2009 - 01:00:03 PDT
