VMD-L Mailing List

From: haider abbas (haiderabbasphy_at_yahoo.co.in)
Date: Wed Apr 27 2005 - 06:28:03 CDT

Dear Axel and Eduard,
thank you very much for your email. I am again writing
in detail so that i could be able to completely remove
the missing bond problem with your help.
i am simulating pressure induced amorphization of
alpha quartz by classical MD and with CPMD. the file
created by classical MD run clearly shows 5,6,7..
coordinated Si atom when it is visualized by "rasmol",
which is confirmed by the previously published
literature. When i visualised the same file with "vmd"
it shows Si atom only four coordinated. I tried the
same option (dynamic bond ) as told by you but when i
increased Distance cutoff, first it start showing
much oxygen-oxygen bond which is not expected and then
it shows increased Si-Si bond. i dont understant what
the value for cutoff should i use so that it may show
the same number of bonds between all atoms as it is
shown by rasmol, Because the file created by CPMD are
in XYZ format and can not be visualized by rasmol and
there is much more option in vmd . Again the second
problem is that the nearly all published paper shows
the snapshots in sphere and lines format which is
equivalent to "CPK" option of vmd. That is why i need
the snapshot in CPK format which must also clearly
show the all bonds between all atoms.
thanks
please spend some time in my help
yours sincerely
Haider Abbas

________________________________________________________________________
Yahoo! India Matrimony: Find your life partner online
Go to: http://yahoo.shaadi.com/india-matrimony