[gmx-users] Orienting molecule in a correct direction

[Justin Lemkul]

On 11/1/16 11:22 AM, faride badalkhani wrote:
> Hi,
>
> You're right. I am sorry for the unclear explanation. I used the editconf
> -princ command and chose ligand as the group for aligning in x direction.
> then I used the editconf -rotate 0 90 0 to align along z. Then I executed
> pdb2gmx command. Then
> editconf -f complex.gro -o complex-box.gro -center 4 4 4 -box 8 8 24
> I want to pull a total distance of 16 nm.

That's not possible with a box that size, unless you use geometry = 
direction_periodic, disable pressure coupling along z, and adjust other pull 
settings accordingly.  The maximum that you can pull in the z-dimension is 12 nm 
with these settings.


> I continued the procedure till generating configurations and this is the
> mdp file for pulling:
>
> title       = Umbrella pulling simulation
> define      = -DPOSRES_A

One thing I will advise (as I keep having to do this privately as people ask 
about my tutorial): do not follow the tutorial too literally.  For general 
protein-ligand complexes, it is *NOT* appropriate to assume one-dimensional 
pulling or applying position restraints to the protein.  Our paper (from which 
the tutorial was derived) describes the somewhat unique case we were dealing 
with.  For a protein-ligand complex, which is spherically symmetrical, treating 
it the same way is inappropriate.

-Justin

> ; Run parameters
> integrator  = md
> dt          = 0.002
> tinit       = 0
> nsteps      = 1000000    ; 1 ns
> nstcomm     = 50
> ; Output parameters
> nstxout     = 5000       ; every 10 ps
> nstvout     = 5000
> nstfout     = 5000
> nstxtcout   = 5000       ; every 1 ps
> nstenergy   = 5000
> ; Bond parameters
> constraint_algorithm    = lincs
> constraints             = all-bonds
> continuation            = yes       ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist     = 5
> ns_type     = grid
> rlist       = 1.2
> rcoulomb    = 1.2
> rvdw        = 1.2
> ; 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
> ; Berendsen temperature coupling is on in two groups
> Tcoupl      = Nose-Hoover
> tc_grps     = Protein_CHL  Water_and_ions
> tau_t       = 0.5       0.5
> ref_t       = 310       310
> ; Pressure coupling is on
> Pcoupl          = Parrinello-Rahman
> pcoupltype      = isotropic
> tau_p           = 1.0
> compressibility = 4.5e-5
> ref_p           = 1.0
> refcoord_scaling = com
> ; 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             = Chain_A
> pull_group1             = Chain_B
> pull_rate1              = 0.1           ; 0.1 nm per ps
> pull_k1                 = 836.8         ; kJ mol^-1 nm^-2
>
> but ater 60000 steps I got the following error:
>
> Distance of pull group 1 (11.850665 nm) is larger than 0.49 times the box
> size 12.092276)
>
> Should I increase all the box dimensions or just z dimension?
>
>
> Regards,
> Farideh
>
>
> On Sun, Oct 30, 2016 at 7:50 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/30/16 12:03 AM, faride badalkhani wrote:
>>
>>> Dear all,
>>>
>>> I want to define z axis as the reaction coordinate in a series of umbrella
>>> sampling simulations. As a first step, I use the editconf -prince to
>>> orient
>>> the ligand along the x axis and then I change the x and z columns in an
>>>
>>
>> x and z columns of what?  If you have an orientation aligned along x, and
>> you want it aligned along z, it's a simple use of editconf -rotate 0 90 0
>>
>> editor. But, every time I get error at pulling step. Could you tell me what
>>> is wrong?
>>>
>>
>> No, because you haven't told us what the exact error is and all the steps
>> you took in between.  There's a lot of work that goes on between setting up
>> an orientation and actually running a simulation.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================