[gmx-users] fail to pull

Albert mailmd2011 at gmail.com
Sun Apr 7 17:17:57 CEST 2013

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?

thank you very much

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