[gmx-users] fail to pull

[Justin Lemkul]

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
>> aligned
>> 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
>> pathway?
>>
>> -Justin
>>
>
> 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

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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