[gmx-users] Final state not reached in pulling simulation
lloyd.riggs at gmx.ch
Thu Jul 12 21:43:28 CEST 2012
your pull force looks insanly high especially if your pulling a small piece of residue? But for a whole protein of averidge 40 KDa, or 350 amino acids its around 2000 to 3000 from liturature (only about 6 that I could find anyways). I might thus be wrong, but wounder if you have a pull rate and force what one wins?
-------- Original-Nachricht --------
> Datum: Thu, 12 Jul 2012 18:15:53 +0200
> Von: Thomas Schlesier <schlesi at uni-mainz.de>
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] Final state not reached in pulling simulation
> 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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