[gmx-users] Final state not reached in pulling simulation
neeru.bioinfo at gmail.com
Thu Jul 12 14:46:17 CEST 2012
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 !!!
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