From: jonathan_at_ibt.unam.mx
Date: Tue Apr 04 2006 - 15:24:31 CDT
Sorry, I thought Himanshu needed images generated with crystal symmetry
operations.
J. Valencia
Quoting Sterling Paramore <paramore_at_hec.utah.edu>:
> Actually, NAMD can do all of the standard crystal types, as they are
> isomorphic with parallelepiped boundary conditions which satisfy certain
> criteria. Check out the gromacs manual (page 13):
> http://www.gromacs.org/documentation/paper_manuals.php, or the DLPOLY
> manual (page 167):
> http://www.cse.clrc.ac.uk/msi/software/DL_POLY/MANUALS/USRMAN2.16.pdf.
> They both have usefull discussions concerning this topic and about how
> to pick the basis vectors. There are some bizarre boundary conditions
> which cannot be reproduced with a parallelepiped (e.g., spherical), but
> most of the time you shouldn't need to worry about it.
>
> -Sterling
>
> jonathan_at_ibt.unam.mx wrote:
>
> >I proposed this as a future implementation in a poll they sent to this list
> a
> >while ago, but I haven't heard anything about the subject (yet), so
> -according
> >to my experience trying to simulate a hexagonal crystal- you'll have to
> switch
> >to CHARMM and bear with it (sorry).
> >
> >If you decide to go for it, don't forget to pay special attention to the
> part of
> >the documentation about the "aligned" and "symmetric" coordinate systems. OR
> you
> >can send me a mail if you start banging your head against the wall trying to
> set
> >up your cristal (it happens...).
> >
> >J. Valencia
> >
> >
> >Quoting Himanshu Khandelia <hkhandel_at_dtc.umn.edu>:
> >
> >
> >
> >>Hello !
> >>
> >>Can NAMD work with periodic boundary conditions of different types, (other
> >>than cubic or orthorhombic) ? For example, a rhombic dodecahedron, or
> >>hexagonal crystal ? If yes, how does one specify the basis vectors ?
> >>thanks !
> >>
> >>-Himanshu
> >>
> >>
> >>
> >
> >----------------------------------------------------------------
> >Este mensaje fue enviado desde el servidor Webmail del Instituto de
> Biotecnologia.
> >
> >
>
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