Hi Pawel,
Thank you for the clarifications.
4. To check if your system is set up correctly one thing you can do is
convert your inpcrd file to a pdb (use ambpdb) and add a CRYST1 pdb format
record. Then in vmd you can use the periodic tab in the
Graphics->Representations window to generate periodic boundy copies of your
system: if all space is neatly tasselated, you are good.
I did that and I got exactly the same tessellation with the two images I
showed before equilibration (with gaps between boxes). This is the line I
added to the .pdb:
CRYST1 106.000 106.000 86.000 90.00 90.00 120.00 P 21 21 21 8
> 6.About your images: is that the same system? Why are there empty spaces
> there between hexagonal shaped boxes? Again, the unit cell should look like
> a triclinic cell and it is only the tasselation in space of those unit
> cells that will create a hexagonal "look". (see attached images)
>
Is it because I start from a hexagonal prism box generated by CHARMM-GUI?
How did you generate the triclinic box you showed? It looks like a hexagon
before wrapping (or "imaging" in AMBER language) water coordinates to the
central cell.
thanks,
Thomas
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Nov 12 2013 - 10:00:02 PST
