[gmx-users] Umbrella Pulling
Thomas Schlesier
schlesi at uni-mainz.de
Fri Feb 17 17:06:05 CET 2012
As far as i remember for PBC the distance between the reference and the
pulled group are relevant, and not the distance between the reference
group and the virtual spring (place where the pulling potential is zero).
Looking into the code of GROMACS-4.0.7 backs this.
If the distance between the reference group and spring would be
relevant, one should see first an increasing force, then when pbc
matters, the force should decrease, because we pull now in the other
direction.
Looking into the code of GROMACS-4.5.4, it seems there is an error
message for pbc violations:
gmx_fatal(FARGS,"Distance of pull group %d (%f nm) is larger than 0.49
times the box size (%f)",g,sqrt(dr2),max_dist2);
pull.c; line 329
One thing is that the force constant for the pulling is quite small, so
probably you need more force the move the ligand? (But i can't really
comment on this, because i can't find your force vs time plot, so i
don't know how large the force actually is).
Greetings
Thomas
>>
>>
>> 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>
>> http://www.bevanlab.biochem.
>>
>> <http://www.bevanlab.biochem./__>____vt.edu/Pages/Personal/__justin
>> <http://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>
>> <http://vt.edu/> | (540) 231-9080<tel:%28540%29%20231-9080>
>> <tel:%28540%29%20231-9080>
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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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