One more detail. When I use in NAMD :
wrapWater on
wrapAll on
wrapNearest off
I get the hexagonal prism I showed, but when I set:
wrapWater on
wrapAll on
wrapNearest off
I get exactly the triclinic box you showed.
On 12 November 2013 19:31, Thomas Evangelidis <tevang3.gmail.com> wrote:
> 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/
>
>
>
--
======================================================================
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 - 13:30:02 PST
