[gmx-users] Umbrella Pulling
Justin A. Lemkul
jalemkul at vt.edu
Fri Feb 17 15:52:04 CET 2012
Steven Neumann wrote:
>
>
> On Fri, Feb 17, 2012 at 2:12 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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?
>
No, it's not. You're doing 1 ns of simulation (contrary to the comment, 500000
* 0.002 = 1000 ps) and thus pulling at 10 nm per ns you are trying to pull 10 nm
in this simulation. So once your molecule hits 6 nm (right at about 600 ps from
your plot and the expected pull rate), you're violating the criterion that I
suspected.
-Justin
>
> 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>
> <mailto: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>
> <mailto: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>
> <mailto: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>>
> <mailto: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/>
> <http://vt.edu/> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> <tel:%28540%29%20231-9080>
> <tel:%28540%29%20231-9080>
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>
> <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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> ------------------------------____----------------------------__--__------------
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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>
> <http://vt.edu/> | (540) 231-9080 <tel:%28540%29%20231-9080>
> <tel:%28540%29%20231-9080>
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> http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
> <http://vt.edu/Pages/Personal/justin>
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> <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://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
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