From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Tue Apr 04 2006 - 14:16:07 CDT
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
>>
>>
>>
>
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