[gmx-users] defining box dimensions in gromacs

[Apurva Sharma]

Hello
     gromacs usrs 

i just start the gromacs. i have some basic questions
releted to Box Dimensions .
Sorry for very big mail and no. of basic questions. !
I start the Simulation of dppc bilayer which i
downloaded   from peter telimen site.
1.  In the 3nd line of dppc.pdb some dimension are
given.so there is any need to specify box dimensions
when i used editconf program.
i used "editconf -f dppc -o dppc " i didnt specify any
box dimension i want to use dimension as it is specify
in pdb  file.
CRYST1   64.184   64.435   65.965  90.00  90.00  90.00
P 1           1
But after this comond it did not report any box
dimension it only report volume.
but my simulation going well . I want to just conform
what box dimension its using ??Is there is any option
from where i can know about box size.

2.  If i used "editconf -f dppc128 -o dppc128 -d 0.0"
then it reports
system size :  6.612  6.639  6.741 (nm)
    center      :  3.195  3.240  3.329 (nm)
    box vectors :  6.418  6.444  6.596 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 272.81               (nm^3)
    shift       :  0.111  0.079  0.042 (nm)
new center      :  3.306  3.320  3.371 (nm)
new box vectors :  6.612  6.639  6.741 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 295.91               (nm^3)

why it reports two times Box dimension .??
what is diffrence between new center and center ??
what is mean by shift ??
what is diffrence between system size and box vector
??

3.  last one if i used "editconf -f dppc128 -o dppc128
-bt cubic -d 0.0" then it reports 
system size :  6.612  6.639  6.741 (nm)
    diameter    : 11.047               (nm)
    center      :  3.195  3.240  3.329 (nm)
    box vectors :  6.418  6.444  6.596 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 272.81               (nm^3)
    shift       :  2.329  2.283  2.195 (nm)
new center      :  5.523  5.523  5.523 (nm)
new box vectors : 11.047 11.047 11.047 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :1348.09               (nm^3)

why there is so much diffrence between above two box
vectors (11.047 and 6.418) ??? and also in volume
(1348.09 and 272.81).??? even though i am using the
same system.
what is mean by dimeter(11.047) here ???

please give me some guide lines .!!!

i am so much Thankfull to all of u ..
 Thanks 

                      Apurva Sharma
                 Indian Institute of Technology Kanpur
                         Chemical Engineering.
                                India.



		
_______________________________
Do you Yahoo!?
Declare Yourself - Register online to vote today!
http://vote.yahoo.com