[gmx-users] Umbrella Pulling

Steven Neumann s.neumann08 at gmail.com
Fri Feb 17 11:44:41 CET 2012 

Would you recommend position restrained of the protein backbone atoms or
e.g. residues from the lower part so that the protien will not roatate?

On Fri, Feb 17, 2012 at 10:41 AM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Hello Justin,
>
> As you recommended I run longer pulling of my ligand. I pull the ligand
> which is on the top of my protein so the top of the protein is pulled so
> that the whole protein rotated app. 30 degrees - the low part of the
> protein came out of the box due to the rotation. After app 600 ps the
> ligand does not move any more and the force applied increase linearly. As I
> saw the trajectory, ligand does not collide with a periodic image but it
> does not move. Please, see attacheg plot force vs time. Can you explain why
> the force increase linearly and ligand is not pulled any more? This is my
> mdp file for pulling:
>
> title       = Umbrella pulling simulation
> ; 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     = 500
> nstxtcout   = 500       ; every 1 ps
> nstenergy   = 500
> ; Bond parameters
> constraint_algorithm    = lincs
> constraints             = all-bonds
> continuation            = yes       ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist     = 5
> ns_type     = grid
> rlist       = 0.9
> rcoulomb    = 0.9
> rvdw        = 0.9
> ; PME electrostatics parameters
> coulombtype     = PME
> fourierspacing  = 0.12
> fourier_nx      = 0
> fourier_ny      = 0
> fourier_nz      = 0
> pme_order       = 4
> ewald_rtol      = 1e-5
> optimize_fft    = yes
> ; Temperature coupling is on
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc_grps     = Protein_LIG Water_and_ions   ; two coupling groups - more
> accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 298   298                     ; reference temperature, one
> for each group, in K
> ; Pressure coupling is on
> Pcoupl          = Parrinello-Rahman
> pcoupltype      = isotropic
> tau_p           = 1.0
> compressibility = 4.5e-5
> ref_p           = 1.0
> ; Generate velocities is off
> gen_vel     = no
> ; Periodic boundary conditions are on in all directions
> pbc     = xyz
> ; Long-range dispersion correction
> DispCorr    = EnerPres
> ; 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     = Protein
> pull_group1     = LIG182
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 200      ; kJ mol^-1 nm^-2
>
> Thank you,
>
> Steven
>
>
>
> On Mon, Feb 13, 2012 at 2:53 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:
>
>> Thank you Justin!
>>
>>
>> On Mon, Feb 13, 2012 at 2:44 PM, Justin A. Lemkul <jalemkul at vt.edu>wrote:
>>
>>>
>>>
>>> Steven Neumann wrote:
>>>
>>>> Thank you Justin. I run my pulling using two force constant for
>>>> pulling. K1=100 and K1=200
>>>> Please, see attached plots of force vs time. Is there any criteria to
>>>> adjust pulling constant? Would you suggest running it for a longer time?
>>>>
>>>
>>> I know of no systematic study for choosing a force constant.  Guessing
>>> wildly at what's going on, I'd say you need longer simulations as it
>>> appears you have only just caused dissociation towards the end of the 500
>>> ps.
>>>
>>> -Justin
>>>
>>> Steven
>>>>
>>>> On Mon, Feb 13, 2012 at 1:11 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>>> jalemkul at vt.edu>> wrote:
>>>>
>>>>
>>>>
>>>>    Steven Neumann wrote:
>>>>
>>>>        Dear Gmx Users,
>>>>         Is it always required to restrained positions of the protein
>>>>        while pulling your ligand? My system is made of 10 ligands
>>>>        attached to my protein surface. I am pulling one of them.
>>>>
>>>>
>>>>    No, it is not required.  I assume you've gotten this idea from my
>>>>    tutorial - the restraints there were used for a very specific
>>>>    purpose (detailed in the paper linked from the tutorial).
>>>>
>>>>
>>>>        I have just seen trajectory of pulling my ligand without
>>>>        restraining positions of protein and 9 remaining ligands. My
>>>>        ligand while pulling also pulled the protein with itself (for 1
>>>>        nm distance) and then splited. Is is this approach more reliable?
>>>>
>>>>
>>>>    If your goal is umbrella sampling, you need only generate a series
>>>>    of reasonable starting configurations along a defined reaction
>>>>    coordinate.  The absolute positions are irrelevant; it is the
>>>>    relative distance that matters.
>>>>
>>>>    -Justin
>>>>
>>>>    --     ==============================**__==========
>>>>
>>>>
>>>>    Justin A. Lemkul
>>>>    Ph.D. Candidate
>>>>    ICTAS Doctoral Scholar
>>>>    MILES-IGERT Trainee
>>>>    Department of Biochemistry
>>>>    Virginia Tech
>>>>    Blacksburg, VA
>>>>    jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>>>    <tel:%28540%29%20231-9080>
>>>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>> >
>>>>
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>>>> ------------------------------**------------------------------**
>>>> ------------
>>>>
>>>>
>>>> ------------------------------**------------------------------**
>>>> ------------
>>>>
>>>>
>>> --
>>> ==============================**==========
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>
>>> ==============================**==========
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>>
>>
>
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