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