On 7/12/12 3:43 PM, lloyd riggs wrote:
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?
The force constant and pull rate do not compete. The pull rate governs how fast
the virtual particle is pulled (at constant velocity) and the stiffness of the
spring dictates the response of the pulled group to which it is attached.
I agree that the force constant seems excessive. I also wonder why the pulling
is only being applied in the z-direction. To the OP - are the GTP and chosen
residue completely linear in the z-direction? Does the protein structure rotate
over time? If it does, then you're doing nonproductive pulling. How are you
measuring the distance (achieved and desired)? Is it the z-component of the
distance only, or the complete distance?
I would also note that one-dimensional pulling using the "distance" geometry is
relatively inflexible. Using "direction" or "position" geometries in concert
with pull_vec1 and/or more sophisticated index groups may be more appropriate.
-Justin
-------- Original-Nachricht --------
Datum: Thu, 12 Jul 2012 18:15:53 +0200 Von: Thomas Schlesier
<schl...@uni-mainz.de> An: gmx-users@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).
greetings thomas
Am 12.07.2012 17:26, schrieb gmx-users-requ...@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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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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