[gmx-users] Umbrella Pulling
Steven Neumann
s.neumann08 at gmail.com
Fri Feb 17 15:45:56 CET 2012
On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Steven Neumann 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:
>>
>>
> Is the pulled distance greater than half of the box vector in z? That's
> the only reason I can see things going haywire. With simple "distance"
> geometry, there are some limitations like that. Rotation itself is not a
> problem. You're separating two objects; there's no clear orientation
> dependence in that case.
>
> -Justin
>
As you can see the pulling distance is 5 nm. The lenght of my box in Z
direction is 12 nm. Thus, it is not. Any other ideas?
>
> 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
>>
>> 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?
>>
>> Thank you,
>>
>> Steven
>>
>>
>>
>>
>>
>>
>>
>> On Fri, Feb 17, 2012 at 10:41 AM, Steven Neumann
>> <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>**> wrote:
>>
>>
>>
>>
>>
>> On Mon, Feb 13, 2012 at 2:53 PM, Steven Neumann
>> <s.neumann08 at gmail.com <mailto: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 <mailto: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>
>> <mailto: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/>
>> <http://vt.edu/> | (540) 231-9080
>> <tel:%28540%29%20231-9080>
>> <tel:%28540%29%20231-9080>
>> http://www.bevanlab.biochem.
>> <http://www.bevanlab.biochem./**>____
>> vt.edu/Pages/Personal/**justin <http://vt.edu/Pages/Personal/justin>
>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin>
>> >
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>> _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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>> ------------------------------**
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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 <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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