[gmx-users] Umbrella sampling COM distance

nahren manuel meetnahren at yahoo.com
Wed Oct 12 15:11:25 CEST 2011

Dear Gromacs Users,

I am trying to study the free energy of binding in a protein-ligand complex. 

I use the following pull input in my mdp file:
; Pull code
pull            = umbrella
pull_geometry   = distance      
pull_dim        = N Y N
pull_start      = yes           
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     = GLC
pull_rate1      = 0.005          
pull_k1         = 1000         

if I am pulling in 'Y' direction, is it necessary to make sure that the distance between the COM (of the protein and ligand) = distance between the Y coordinates,  i.eY(pro)-Y(lig),  ?

---- VMD commands ----

set pro [atomselect top "protein"]

set glc [atomselect top "resname GLC"]

set A [measure center $pro weight mass]
40.33518600463867 35.01163101196289 38.7291374206543

set B [measure center $glc weight mass]
40.591331481933594 39.440189361572266 38.494876861572266

vecdist $A $B

Y(pro)-Y(lig) = 4.42855835

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