[gmx-users] fail to pull

[Jianguo Li]

You switched on the position restraint in your mdp file, is that the reason?


________________________________
 From: Albert <mailmd2011 at gmail.com>
To: gromacs maillist <gmx-users at gromacs.org> 
Sent: Sunday, 7 April 2013, 2:47
Subject: [gmx-users] fail to pull
 
Dear:

I am trying to pull my ligand outside of the binding pocket with following configurations:

title       = Umbrella pulling simulation
define      = -DPOSRES
; Pull code
pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = Y N N
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Protein
pull_group1     = LIG
pull_rate1      = 0.001      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000      ; kJ mol^-1 nm^-2

Tcoupl      = v-rescale
tc_grps     = Protein_LIG   Water_and_ions
tau_t       = 0.5       0.5
ref_t       = 310       310
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 1.0   1.0
compressibility = 4.5e-5
ref_p           = 1.0     1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel     = no
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres



It is quite strange, the ligand is still in place and not outside the pocket at the end of simulations. I am just wondering where is the problem?

thank you very much
best
Albert

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