[gmx-users] Fw: lipid pulling

[xy21hb]

Dear all,

I am pulling the saturated and unsaturated chains of a lipid bilayer to "simulate" its gel phase transition by pull code. It ends with the expected extended structure.

But when I continue with zero pulling rate
to maintain the extended structure for a while, the tails go back to the original length.
I guess I have made some mistakes in the mdp pull code part,

=========
pull                    = umbrella
pull-ngroups            = 6
pull-ncoords            = 4

pull-group1-name        = topC2
pull-group2-name        = downC2
pull-group3-name        = topC218
pull-group4-name        = downC218
pull-group5-name        = topC316
pull-group6-name        = downC316

pull-geometry    = distance      ; simple distance increase

pull-coord1-groups      = 1 3
pull-coord2-groups      = 1 5
pull-coord3-groups      = 2 4
pull-coord4-groups      = 2 6
pull-dim         = N N Y

pull-coord1-vec         = 0 0 1
pull-coord1-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
pull-coord1-k           = 1000          ; kJ mol^-1 nm^-2
pull-coord2-vec         = 0 0 1
pull-coord2-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
pull-coord2-k           = 1000          ; kJ mol^-1 nm^-2
pull-coord3-vec         = 0 0 1
pull-coord3-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
pull-coord3-k           = 1000          ; kJ mol^-1 nm^-2
pull-coord4-vec         = 0 0 1
pull-coord4-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
pull-coord4-k           = 1000          ; kJ mol^-1 nm^-2

pull-coord1-init        =  1.0
pull-coord2-init        =  1.0
pull-coord3-init        =  1.0
pull-coord4-init        =  1.0

pull-start       = yes         ; define initial COM distance > 0

============

Any guess on the reason? Many thanks.

 
Best,

Yao
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