VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Fri Dec 09 2005 - 01:32:31 CST

hi vmd'ers

> Therefore, I would suggest that your first three items (i.e., those dealing
> with non covalently bonded atoms) are more relevant to most of us than the
> other three. But it would certainly be interesting to read the opinion of
> other VMD users on this list.
i work on several different projects (in terms of methodology, programs
used, systems studied ...) and these have different needs

for biomolecular simulations or simulations of similar types, jerome
definitely identified the most important features.

however, for material simulations and generally work connected with
crystals/solids/infinite systems, automatic bond search across PBC cell
boundaries is really missing (+ the last 2 features from the list, of
course). with respect to this, adding another checkbox 'display unit
cell' for showing unit cell vectors / parallelopiped (or whatever the
cell looks like) would also improve the usability of vmd for
material/crystal related work.

>>Adding PBC-awareness to the drawing code is the most risky in terms
>>of hurting performance, but this may be something that could be dealt with
>>by adding a checkbox so that VMD only spends effort checking for this when
>>the user actually needs it.
definitely a good idea!

i don't know how many people using vmd are in the crystal/solid
business, but i find all features of the same importance (maybe the
second half is even more important for me since i'm now doing more
crystals than proteins :)

regards,
lubos 

-- 
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Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
http://www.molecular.cz/~vrbka
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