[gmx-users] about the Umbrella input file!

[nanyu101 at sina.com]

Dear gmx-users,

   Now, I want to do some dynamics for my zinc enzyme. At the beginning, I do want to use umbrella sampling or constraint method to keep the coordination ligands of metal. I have done two tests.
First, I do constraint the distance between one ligand and metal cation,the running is just fine and my ppa input was listed here.

erbose           = no
runtype           = umbrella
group_1           = SUR
reference_group   = ZN
reftype           = com
reflag            = 1
constraint_direction = 0.0 0.0 0.0
constraint_tolerance = 0.001
k1                = 1000
pos1              = 0.0 0.0 0.0


Second, I do want to constraint all the distances between the coordination ligands and metal cation, but I failed. The ppa input file was listed here. I do not know the reason? The program can\'t read the group_2, group_3, pos2 and pos3.

erbose           = no
runtype           = umbrella
group_1           = SUR
group_2           = NB1
group_3           = NB2
reference_group   = ZN
reftype           = com
reflag            = 1
constraint_direction = 0.0 0.0 0.0
constraint_tolerance = 0.001
k1                = 1000
k2                = 1000
k3                = 1000
pos1              = 0.0 0.0 0.0
pos2              = 0.0 0.0 0.0 
pos3              = 0.0 0.0 0.0

Thank you very much.

all your bests,
nanyu
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