Re: other crystal types in NAMD ?

From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Tue Apr 04 2006 - 15:13:29 CDT

If that's the case, then I'm sure someone's written a tcl script to do
it with VMD.

-Sterling

jonathan_at_ibt.unam.mx wrote:

>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.
>>
>>
>>>
>>>
>
>
>
>
>----------------------------------------------------------------
>Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia.
>
>

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