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From: sharvil kaware (sharvil_kaware_at_yahoo.co.in)
Date: Fri Jun 11 2010 - 16:10:15 CDT

Good evening everybody.
I am trying to simulate 40 Angstrom diameter  water droplet evaporation using NAMD.The sphere is  centrally enclosed in 100x100x 100 cubic Angstrom  water box for applying periodic boundary conditions. Centre of box and sphere is at origin (0,0,0). I wish to provide  water vapour surrounding for my system.For this, I plan to stretch cell basis vector in Z-direction using follwing configuration.
# Periodic Boundary Conditions
cellBasisVector1    100.    0.   0.
cellBasisVector2     0.   100.   0.
cellBasisVector3     0.    0    124
cellOrigin                0.    0.    0.

# PME (for full-system periodic electrostatics)
PMEGridSizeX        101
PMEGridSizeY        101
PMEGridSizeZ        125 
 
I would like to know whether this approach is right and if it is OK,  how is the length of cell basis vector  considered in NAMD? I mean  is the value of cell basis vector in Z direction (i.e.124 ) will be measured from  origin(centre of box)? or does this mean that unit cell in Zdirection will be placed at 124 Angstroms from centre of box? 
I will greatly appreciate if someone shares his/her views in this regard.
 
Thank You,
With High Regards
Ravindra Kaware
Ph.D. candidate,
North Carolina A &T State University 
Greensboro, NC USA

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