[gmx-users] Re: fail to pull

[Thomas Schlesier]

Must get the bus, so only short answer.
You could try to use constraint pulling instead of an umbrella 
potential. Then the ligand should move 1nm in 1ns. And you could see is 
the setup is ok, or if it would be better to pull into another direction...
greetings
thomas


Am 07.04.2013 18:05, schrieb gmx-users-request at gromacs.org:
>>> 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