Observe water molecules that close to LIG(lipid):

all and within 5 of resname LIG

display resize 800 600

output dcd trajectory

set s1 [atomselect top all]

animate write dcd tmp.dcd waitfor all $s1

exiCATDCD: http://www.ks.uiuc.edu/Development/MDTools/catdcd/ extract certain frames from a trajectory: catdcd -o output.dcd -first ??? -last ??? input.dcd
Here is one website that have many vmd applications: http://hi.baidu.com/sobereva/item/c23f2edeba7400312b35c7dd

display cell dimesion:

set cell [molinfo $molid get {a b c} frame $frame] 

this is more acurate than

measure minmax .....

display atom selected:

mol delrep 0 top

set selection1 [atomselect $molid "water within 5 of name MG or water within 5 of name 'Cl-' or water within 5 of name AL or water within 5 of name 'Na+'"]

mol selection "[$selection1 text]"

mol addrep top