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

Thomas Schlesier schlesi at uni-mainz.de
Thu Jul 12 18:15:53 CEST 2012

It could be possible tht you do not pull into the 'right' direction. if 
there is another group between 'GTP' and 'Residue' you will get clashes 
and 'Residue' won't move further (could be a water molecule, or some 
other part of 'GTP').
If this happens you should observe an increase in the force due to the 
umbrella potential.
If the problems are due to waters molecules which block the 'pathway' 
you could just delete them.
If another group is in the way, you might want to change the pull-vector 
(and if lucky find the right one). But don't know what would be the best 
strategy in this case. Maybe you can look into what docking-people do, 
seems to me that your simulation is related to what they do (but myself 
has absolute no knowledge about docking simulations).


Am 12.07.2012 17:26, schrieb gmx-users-request at gromacs.org:
> 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 !!!
> Thanks,
> Neeru Sharma

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