[gmx-users] fail to pull
jalemkul at vt.edu
Sun Apr 7 17:31:21 CEST 2013
On Sun, Apr 7, 2013 at 11:17 AM, Albert <mailmd2011 at gmail.com> wrote:
> On 04/06/2013 08:52 PM, Justin Lemkul wrote:
>> Hard to tell. Does your ligand have a suitable exit pathway exactly
>> along the x-axis? Have you tried increasing the pull rate? How long is the
>> simulation? I don't even see nsteps in the above .mdp file. How about
>> increasing the force constant? Is the vector connecting the COM of the
>> entire protein and the COM of the ligand suitable for describing the exit
> Hello Justin:
> thanks a lot for kind rely.
> Yes, I adjust the conformation of whole protein/ligand so that it can
> exist from X-axies. I only show part of the .mdp file so some of then are
> not shown.
> ; Run parameters
> integrator = md
> dt = 0.002
> tinit = 0
> nsteps = 500000 ; 500 ps
> nstcomm = 10
> ; Output parameters
> nstxout = 5000 ; every 10 ps
> nstvout = 5000
> nstfout = 1000
> nstxtcout = 1000 ; every 1 ps
> nstenergy = 1000
> probably I should consider use part of the protein such as residues around
> binding pocket as COM for protein instead of whole protein? I applied for
> 1ns with rate pull_rate1= 0.001, so at then end of pulling, the distance
> for COMprotein and COM ligand should be 10A. Probably this is too short for
> whole protein as COM?
Let me clear one thing up first. 1 ns of pulling with a 0.001 nm/ps pull
rate will not necessarily cause the ligand to be displaced by 1 nm. The
particle pulling the virtual spring will be displaced by 1 nm, but the
ligand will only move as a function of this applied force and the restoring
forces (i.e. interactions between the ligand and protein).
Choosing a more suitable reference group and running the simulation for
longer will produce the desired result.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540)
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