AMBER Archive (2008)

Subject: RE: AMBER: periodic boundary condition

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 23 2008 - 22:09:39 CDT

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
>
>
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