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).
greetings
thomas
Am 12.07.2012 17:26, schrieb [email protected]:
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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