[gmx-users] Final state not reached in pulling simulation

neeru sharma neeru.bioinfo at gmail.com
Wed Jul 11 10:18:43 CEST 2012

Hello all,

I m performing a pulling simulation on my Protein-Mg-GTP complex. I
have considered pulling between the GTP and a residue of protein.
The pull code in the .mdp file im using is as follows:

; Pull code
pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = GTP
pull_group1     = Residue
pull_rate1      = -0.00005      ; 0.00005 nm per ps = .05 nm per ns
pull_k1         = 10000      ; kJ mol^-1 nm^-2

The initial distance between GTP and the residue was 7 A and the
desired one was 3A. After the completion of run (10ns), I could get a
trajectory where the final distance was still 4.25 A.

I tried to continue the simulation for another 10ns with the same
value for pull_k1 parameter and one by increasing the value to 100,000
also. In both of the case, the  trajectories showed the distance
stabilized near _4.25 A only.
Can anyone please tell me the reason behind it? What should I do, so
that I could get the desired distance ?

Any suggestion and help is welcome !!!


Neeru Sharma

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